Re: [Freesurfer] Correcting defect

[Katarina Trojacanec]

Thank you.
I have uploaded the files (lh.inflated_TP_1_4.nofix and 
lh.inflated_TP_2_4.nofix). 

What should I do as a next step?

Cheers
Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Wednesday, May 4, 2016 2:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correcting defect

sure. Or you can load the ?h.inflated.nofix and look at it - it should be
obvious if there is a huge defect (you can also load the file
?h.defect_labels as an overlay on that surface and it will show you the
segmentation of the defects)

cheers
Bruce
On Wed, 4 May 2016, Katarina Trojacanec wrote:

>
> Dear FreeSurfer Team,
>
>
> I have been trying to run creation of template with FreeSurfer. However,
> for two cases for one patient (case 1: template based on TP1 and TP4, case
> 2: template based on TP2 and TP4), the correcting defect step is running
> too long. According to the information in the mail archive, the defects are
> probably too big, and that is the reason for the long processing.
>
>
> May I send you via ftp the subjects directories so you can help me to
> proceed with this subject, because I am not able to figure out and correct
> the problem? Should I send you the base directories in their current state
> or the cross-sectionally processed time points as well?
>
>
> Best Regards,
>
>
> Katarina Trojacanec, M.Sc.
> Teaching and research assistant
>
> Faculty of Computer Science and Engineering
> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
>
>
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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas Greve]

Underneath, they both use the same code, so they should give the same 
results. Are you saying they are different? I don't know what SurfFWHM 
is doing so I can't comment on what those results mean. Measuring the 
FWHM on the surface is quite tricky.

doug


On 5/4/16 6:41 PM, Ajay Kurani wrote:

Hi Freesurfer Experts,
   I am trying to understand the difference between qcache option and 
mris_fwhm and which is appropriate for a cortical thickness analysis.  
I processed my  files with qcache and have 
lh.thickness.fsaverage.fwhm15.gii (converted) files.  I used an afni 
tool SurfFWHM to estimate the smoothness of a subject at when looking 
at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was 
approximately 9.3-9.9 smoothness level.


I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i 
lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and 
when using SurfFWHM on the smae subject the smoothness was estimated 
at 11.25.



1) I am not sure if the qcache or the mris_fwhm file is more 
appropriate to use for a cortical thickness analysis.


2) For qdec if I select the 15mm  option does it assume the smoothness 
is 15mm when calculating monte carlo corrections?  Would there be a 
different way to estimate this since my smoothness at 15mm is closer 
to 10mm?


Thanks,
Ajay


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Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Bruce Fischl]

Hi Bronwyn

it depends on the type of stats, but you would either map the Yeo 
annotations to your subjects, or map the stats from your subjects to 
fsaverage.

cheers
Bruce


On Thu, 5 May 2016, Bronwyn Overs wrote:

> Hi Freesurfer Mailing List,
>
> I wish to extract stats for my sample for the Yeo 2011 cortical parcellations 
> and the Choi 2012 striatal parcellations (7 networks) that are provided for 
> download on the freesurfer wiki. My questions are as follows:
>
> 1. I noticed that the Yeo 2011 annot files are already available in 
> fsaverage/label. How do I map these annot file to each of my subjects so that 
> I can extract stats?
> 2. For the Choi 2012 files I wish to use 
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How do I 
> map this file to each of my subjects so that I can extract stats for the 
> 7Network parcellation?
>
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Re: [Freesurfer] Correcting defect

[Bruce Fischl]

Hi Katarina

if you want us to look you need to upload the entire subject dirs (tarred 
and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D 
mode and just see what the big defects look like. If you load the 
orig.nofix at the same time you can goto a vertex in the big defect you see 
on the inflated by typing its index into the info winwo for the orig.nofix. 
This will be automated in v6

Bruce


On Thu, 5 May 2016, Katarina Trojacanec wrote:

> Thank you.
> I have uploaded the files (lh.inflated_TP_1_4.nofix and 
> lh.inflated_TP_2_4.nofix).
>
> What should I do as a next step?
>
> Cheers
> Katarina Trojacanec, M.Sc.
> Teaching and research assistant
>
> Faculty of Computer Science and Engineering
> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: Wednesday, May 4, 2016 2:35 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Correcting defect
>
> sure. Or you can load the ?h.inflated.nofix and look at it - it should be
> obvious if there is a huge defect (you can also load the file
> ?h.defect_labels as an overlay on that surface and it will show you the
> segmentation of the defects)
>
> cheers
> Bruce
> On Wed, 4 May 2016, Katarina Trojacanec wrote:
>
>>
>> Dear FreeSurfer Team,
>>
>>
>> I have been trying to run creation of template with FreeSurfer. However,
>> for two cases for one patient (case 1: template based on TP1 and TP4, case
>> 2: template based on TP2 and TP4), the correcting defect step is running
>> too long. According to the information in the mail archive, the defects are
>> probably too big, and that is the reason for the long processing.
>>
>>
>> May I send you via ftp the subjects directories so you can help me to
>> proceed with this subject, because I am not able to figure out and correct
>> the problem? Should I send you the base directories in their current state
>> or the cross-sectionally processed time points as well?
>>
>>
>> Best Regards,
>>
>>
>> Katarina Trojacanec, M.Sc.
>> Teaching and research assistant
>>
>> Faculty of Computer Science and Engineering
>> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
>>
>>
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Extracting BOLD from a flattened surface

[Douglas Greve]

So you have 1 column, but you want 1 column for each vertex? We don't 
have anything to do that, but you can do it in matlab, eg,

M = fast_vol2mat(MRIread('lh.yourdata.mgh'));
M will be a 240x127000 matrix

On 5/4/16 8:36 PM, Taha Abdullah wrote:

Hello Doug,

Sorry for the confusing and long email, I am interested in extracting 
the raw BOLD signal from a processed 4D nifit file. After registering 
the functional to ${subject}/mri/orig.mgz and generating the 
registration file, I proceeded to convert the functional image to the 
same dimensions as the lh.inflated surface via mri_vol2surf so the 
functional data image now has 127000 x 1 x 1 x 240. So I ran 
mri_segstats command to extract the bold signal, but I ended up having 
240 rows and 1 column in the text file...the ultimate goal is to 
quantify the wave propagation of the BOLD time series across a 
flattened patch. Any advice would be greatly appreciated.


Thanks!

On Wed, May 4, 2016 at 2:26 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



Sorry, can you tell me what you are trying to do? You just want a
number
of time points -by- number of vertices file? Then mri_vol2surf
should do
that for you. Flattening is irrelevant for this as it only changes the
xyz coordinate of the vertex and not the vertex identity.
doug


On 04/29/2016 11:24 AM, Taha Abdullah wrote:
> Hello Freesurfer Experts,
>
> Long story short--I would like to extract BOLD values from each TR
> across all vertices for one subjects flattened surface
> Following is a brief overview of my steps and at the end you can see
> where I am stuck.
> First, after */recon-all /I* followed the steps to cut the lh
inflated
> surface, saved as a patch, ran /*mris_flatten, */converted patch
into
> asc file.
> Second, I used read_patch.m to extract all spatial information and a
> net loss of approximately 10k vertices (127k to 116k)
>
> We had all functional images processed in FSL, the 4D file has
> 64x64x36x240 dimensions (voxels are 3.4x3.4x3.0). Next,
co-registered
> the functional and anatomicals together via the following cmd:
> */ bbregister --s cbp001_v1 --mov filtered_func_data.nii.gz --bold
> --init-fsl --reg dummy1.da/*t. Afterwards, converted the volume to a
> surface using the following cmd*/: mri_vol2surf --mov
> filtered_func_data.nii.gz --reg dummy1.dat --projfrac 0.5 --interp
> trilinear --hemi lh --o ./lh.func.vol2surf.mgh. /*THe dimensions are
> 127027 x 1 x 1 x 240. Visually no problem when using*/ tksurfer
> cbp001_v1 lh inflated -patch /path to flattened patch/ -overlay
> /lh.func.vol2surf.mgh/  -timecourse lh.func.vol2surf.mgh;/* click on
> the patch and shows the timecourse for that selected vertex. Using the
> View>Configure>overlay I can shuffle through the TRs to inspect the
> change in raw BOLD signal per vertex.
>
> I have been perusing the email web server searching for how to
extract
> the hemodynamic waveform for each vertex across the flattened
surface
> and ultimately will be using matlab to understand how the spatial
> transformation is happening. As well I have all the matlab files
that
> seemed relevant to my query (read_surf.m, read_patch.m, and
> readMRI.m). I was hoping that I would be able to have a text
file with
> all the vertices (127K not the flattened 116k) in rows and each
column
> would have the TRs; I ran this command;*/ mri_segstats --slabel
> cbp001_v1 lh
> /home/share/freesurfer/subjects/cbp001_v1/label/lh.cortex.label
> --avgwf mri_seg_stats.dat --i lh.func.vol2surf.mgh/*, output was the
> 240 TRs as rows and seems like the average global BOLD signal in the
> single column corresponding with each TR. Excuse my naiveness, I
just
> recently (1 month ago) started using freesurfer and I feel like
I have
> exhausted as much of the information available on the FS wiki and
> email server. Any information or advice would be great! I put the
> commands just to give an idea of my workflow (most of the command
> lines are from the email server or the FS Wiki) and if there are any
> issues with my steps please let me know so I can correct them before
> starting the group analysis.
>
> Best,
> Taha
>
> --
> Taha Abdullah
> Department of Physiology
> Northwestern University
> Masters of Science Physiology and Biophysics, Georgetown
University 2015
>
>
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> 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-

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Douglas Greve]

On 5/4/16 11:40 PM, Bronwyn Overs wrote:

Hi Freesurfer Mailing List,

I wish to extract stats for my sample for the Yeo 2011 cortical 
parcellations and the Choi 2012 striatal parcellations (7 networks) 
that are provided for download on the freesurfer wiki. My questions 
are as follows:


1. I noticed that the Yeo 2011 annot files are already available in 
fsaverage/label. How do I map these annot file to each of my subjects 
so that I can extract stats?

Use mri_surf2surf with the --save-annot option
2. For the Choi 2012 files I wish to use 
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . 
How do I map this file to each of my subjects so that I can extract 
stats for the 7Network parcellation?

I don't know about this file. Where is it? Is it something we distribute?
doug


--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to 
the NeuRA Magazine 




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Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

Hi Doug, the Choi file is a striatal functional connectivity atlas which we
distribute. It's under the average directory.

Hi Bronwyn,

To transform the Choi's striatal atlas to your individual subject, Here's a
(non-ideal) suggestion I previously suggested to another user:

1) Assuming you are quite happy with the freesurfer striatal parcellation
in your individual subjects, then I am assuming freesurfer nonlinear
registration (talairach.m3z) is working quite well. Talairach.m3z warps
your subject to an internal freesurfer space (kinda like MNI305, but not
quite). Let's say the freesurfer recon-all output is at
/SUBJECT_FS/

2) Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the MNI152
1mm template to the internal freesurfer space. Let's say the freesurfer
recon-all output is at /MNI152_FS/

3) Then do the following:

a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest

b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z
talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph

This is not optimal because of the double interpolation. You might want to
use the MNI template instead of the Choi_atlas to test the above, so you
can check the goodness of the warp. The final warped MNI template should
hopefully look identical to your subject. If that works, then use the
Choi_atlas. Note that mri_vol2vol does not work properly for
talairach.m3z below
version 5, so you should use version 5x mri_vol2vol.

Regards,

Thomas

On Thu, May 5, 2016 at 10:24 PM, Douglas Greve 
wrote:

>
>
> On 5/4/16 11:40 PM, Bronwyn Overs wrote:
>
> Hi Freesurfer Mailing List,
>
> I wish to extract stats for my sample for the Yeo 2011 cortical
> parcellations and the Choi 2012 striatal parcellations (7 networks) that
> are provided for download on the freesurfer wiki. My questions are as
> follows:
>
> 1. I noticed that the Yeo 2011 annot files are already available in
> fsaverage/label. How do I map these annot file to each of my subjects so
> that I can extract stats?
>
> Use mri_surf2surf with the --save-annot option
>
> 2. For the Choi 2012 files I wish to use
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How do
> I map this file to each of my subjects so that I can extract stats for the
> 7Network parcellation?
>
> I don't know about this file. Where is it? Is it something we distribute?
> doug
>
> --
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> [image: Follow NeuRA on facebook]
> [image: Subscribe
> to the NeuRA Magazine] 
>
>
> ___
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] no recon button

[Ani Varjabedian]

Hi Sarah,

If you are using 5.1 you only have one button for editing, the head with 
the pencil in it, like you shared in your screenshot. If you click on 
that it will open up a box that is titled "voxel editing", but you 
should also see a checkbox at the top of it for "recon editing"  (I 
attached a screenshot). If you click the checkbox you will see that the 
brush value gets set to 255 and the erasure value gets set to 1.  This 
is recon editing mode and it locks in the values 255 and 1 because these 
are the values that FS looks for when you re-run the subject to see if 
the user made any changes. If you accidentally edited with different 
values, (say 0 instead of 1) this is where you could "run into problems 
down the line".


In newer versions of freeview, we have two buttons for editing (attached 
screenshot). One that is just for editing the aseg (which we call voxel 
edit), and a separate button for recon editing  that looks like a head 
with an R in it. So in newer versions, if you want to recon edit, you 
just click on the head with an R and it automatically puts you in "recon 
mode".


Does this make sense?

You can try downloading the latest version of freeview to see what I 
mean. But you should be fine using the version you have, just make sure 
to click the checkbox for "recon editing" so that your brushes are set 
to the right values!


Hope this helps,
Ani

On 05/04/2016 08:34 PM, Bruce Fischl wrote:

Hi Sarah

no, I don't think it is. The recon edit for example will set voxels to
"1" not "0" when erase so that we can keep track of them. If you are
editing as part of the recon-all stream you are better off using it than
just plain voxel editing.

cheers
Bruce
On Wed, 4 May 2016, Burke,Sarah E wrote:


Douglas, can you please let me know if the voxel edit button is appropriate to 
use in place of the recon edit?

Thanks,

Sarah

Sent from my iPhone


On May 3, 2016, at 3:04 PM, Burke,Sarah E  wrote:


Is this information correct?


On May 2, 2016, at 3:55 PM, Burke,Sarah E  wrote:

https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html


From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Douglas N Greve 
Sent: Monday, May 2, 2016 3:49 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] no recon button

Can you send us a link to the email you are speaking about?


On 05/02/2016 03:29 PM, Burke,Sarah E wrote:
It opens a box that says "voxel edit" This allows me to edit the images 
accordingly, however I read in the email forum that this may create some issues further 
on down the line?


From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Douglas N Greve 
Sent: Monday, May 2, 2016 3:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] no recon button

what happens when you click on the button with the pencil in it? The one
just above the "S" in "Surfaces"


On 05/02/2016 02:58 PM, Burke,Sarah E wrote:




*From:* freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Douglas Greve

*Sent:* Monday, May 2, 2016 2:31 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] no recon button
Can you send a snapshot of your Freeview window? The Recon Edit button
looks like a sagittal slice with an "R" in it and a pencil pointing to it.


On 5/2/16 1:44 PM, Burke,Sarah E wrote:
Thank you Douglas. However, in the tutorial for editing output, it
says to use the recon edit button to manually perform edits. After
this step, I use the command line and recon-all. How do I do the
manual edits without this button. I do see a voxel edit button.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview



FsTutorial/PialEdits_freeview - Free Surfer Wiki

surfer.nmr.mgh.harvard.edu
top | previous Correcting Pial Surfaces. To follow this exercise
exactly be sure you've downloaded the tutorial data set before you
begin. If you choose not to ...





*From:* freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Douglas Greve

*Sent:* Monday, May 2, 2016 1:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] no recon button
freeview does not have a recon button. You have to run recon-all from
the command line.


On 5/2/16 12:14 PM, Burke,Sarah E wrote:
Hello,


I searched the mail list and saw that others have had this problem,
but I see no answers to their queries. I have version 1.0
(5/13/2013) of Freeview for Linux.  I have no recon button. What
should I do?


Thank you



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Re: [Freesurfer] no recon button

[Burke,Sarah E]

Yes. Thank you!

Sent from my iPhone

> On May 5, 2016, at 11:09 AM, Ani Varjabedian  wrote:
> 
> Hi Sarah,
> 
> If you are using 5.1 you only have one button for editing, the head with the 
> pencil in it, like you shared in your screenshot. If you click on that it 
> will open up a box that is titled "voxel editing", but you should also see a 
> checkbox at the top of it for "recon editing"  (I attached a screenshot). If 
> you click the checkbox you will see that the brush value gets set to 255 and 
> the erasure value gets set to 1.  This is recon editing mode and it locks in 
> the values 255 and 1 because these are the values that FS looks for when you 
> re-run the subject to see if the user made any changes. If you accidentally 
> edited with different values, (say 0 instead of 1) this is where you could 
> "run into problems down the line".
> 
> In newer versions of freeview, we have two buttons for editing (attached 
> screenshot). One that is just for editing the aseg (which we call voxel 
> edit), and a separate button for recon editing  that looks like a head with 
> an R in it. So in newer versions, if you want to recon edit, you just click 
> on the head with an R and it automatically puts you in "recon mode".
> 
> Does this make sense?
> 
> You can try downloading the latest version of freeview to see what I mean. 
> But you should be fine using the version you have, just make sure to click 
> the checkbox for "recon editing" so that your brushes are set to the right 
> values!
> 
> Hope this helps,
> Ani
> 
>> On 05/04/2016 08:34 PM, Bruce Fischl wrote:
>> Hi Sarah
>> 
>> no, I don't think it is. The recon edit for example will set voxels to
>> "1" not "0" when erase so that we can keep track of them. If you are
>> editing as part of the recon-all stream you are better off using it than
>> just plain voxel editing.
>> 
>> cheers
>> Bruce
>>> On Wed, 4 May 2016, Burke,Sarah E wrote:
>>> 
>>> Douglas, can you please let me know if the voxel edit button is appropriate 
>>> to use in place of the recon edit?
>>> 
>>> Thanks,
>>> 
>>> Sarah
>>> 
>>> Sent from my iPhone
>>> 
 On May 3, 2016, at 3:04 PM, Burke,Sarah E  wrote:
 
 
 Is this information correct?
 
> On May 2, 2016, at 3:55 PM, Burke,Sarah E  wrote:
> 
> https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Monday, May 2, 2016 3:49 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] no recon button
> 
> Can you send us a link to the email you are speaking about?
> 
>> On 05/02/2016 03:29 PM, Burke,Sarah E wrote:
>> It opens a box that says "voxel edit" This allows me to edit the images 
>> accordingly, however I read in the email forum that this may create some 
>> issues further on down the line?
>> 
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: Monday, May 2, 2016 3:26 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] no recon button
>> 
>> what happens when you click on the button with the pencil in it? The one
>> just above the "S" in "Surfaces"
>> 
>>> On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
>>> 
>>> 
>>> 
>>> 
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>  on behalf of Douglas Greve
>>> 
>>> *Sent:* Monday, May 2, 2016 2:31 PM
>>> *To:* freesurfer@nmr.mgh.harvard.edu
>>> *Subject:* Re: [Freesurfer] no recon button
>>> Can you send a snapshot of your Freeview window? The Recon Edit button
>>> looks like a sagittal slice with an "R" in it and a pencil pointing to 
>>> it.
>>> 
 On 5/2/16 1:44 PM, Burke,Sarah E wrote:
 Thank you Douglas. However, in the tutorial for editing output, it
 says to use the recon edit button to manually perform edits. After
 this step, I use the command line and recon-all. How do I do the
 manual edits without this button. I do see a voxel edit button.
 
 https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
 
 
 
 FsTutorial/PialEdits_freeview - Free Surfer Wiki
 
 surfer.nmr.mgh.harvard.edu
 top | previous Correcting Pial Surfaces. To follow this exercise
 exactly be sure you've downloaded the tutorial data set before you
 begin. If you choose not to ...
 
 
 
 
 

Re: [Freesurfer] Resting-state fcMRI analysis with GLM

[Eun Young Choi]

Thanks, Doug.

I'm still a little unclear about how to set up a timeseries regressor (120
timepoints) in the design matrix while also specifying the # of subjects
(500). Would the design matrix be a 500x120 or 120x500?

I should mention that my ultimate goal is to find a statistically sig.
threshold for a cortical fcMRI map with 500 subjects. Traditional
correction for multiple comparisons, like Bonferroni and FDR, are not
sufficient. So I'd now like to find a cluster size-based correction
threshold using mri_glm-sim. Hence, my desire to create the cortical fcMRI
map using mri_glmfit, so I can get the files needed for mri_glm-sim. Is
this an okay approach, or is there a better way to do this?

Thank you so much,
Eun Young



On Wed, May 4, 2016 at 3:15 PM, Douglas N Greve 
wrote:

> We don't usually use mri_glmfit for this kind of thing. If you want to
> do it this way, then you cannot use an FSGD file. Instead, create a
> design matrix with the seed time course then pass that to mri_glmfit
> with the --X option (and no --fsgd option).
>
> On 05/04/2016 10:17 AM, Eun Young Choi wrote:
> >
> > Hi all,
> >
> > I'd like to run a resting-state fcMRI analysis within the GLM
> > (mri_glmfit), but I'm not completely sure how to set this up in the
> > FSGD file. I've seen the online tutorial of age vs cortical thickness,
> > but I'm not sure how to specify a regressor with a timeseries. Does
> > anyone have an example of an FSGD file for this?
> >
> > Thanks!
> > Eun Young
> >
> >
> >
> > ___
> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 

*Eun Young Choi, PhD*

Post-doctoral Associate

University of Rochester Medical Center

601 Elmwood Ave, Box 711

Rochester, NY 14642

cell: 551-580-1572
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[Freesurfer] Volumetric measurments and difference between results from "recon_all" and "mri_segstats"

[Saeed Mahdizadeh Bakhshmand]

Hello Folks,

 I used the recon-all -i -all -segmentation for the structural
image. FreeSurfer makes several folder and one of them is "stats". In this
folder, there is aseg.stats that includes volume of different brain
regions. Also, I found "mri_segstats" command line that gives us the volume
of the same brain regions. But, there is significant difference between
reported numbers  from these two methods . I would say the difference is
approximately 200 mm3 for each brain region. Do you know what is correct
way to measure volume of segmented brain regions using FreeSurfer?

Cheers,
Saeed
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[Freesurfer] Customized ColorLUT - opacity value that will make regions totally transparent?

[DeCross, Stephanie N.]

Hi all,

I’m trying to open a couple aseg.mgz labels and color code them. I thought I’d 
do this by making my own ColorLUT table, setting the color of my regions, and 
then making every other region in the table be completely transparent by 
fiddling with the opacity value. I can’t figure out what number I want in the 
opacity column to make a region totally transparent, and on the wiki it says 
something about “255-alpha” for that column, but I don’t know what that means. 
In the opacity column I’ve tried values 0, 1, and 255, and it all looks the 
same (completely opaque) - anyone know what value I want there?

Attached is my ColorLUT table, which currently gives me yellow caudate and 
green amyg and hippo (what I want), and the rest of the aseg.mgz labels are all 
black (I’m trying to change all the black to 100% transparent so they don’t 
show up at all and all I see are my yellow and green regions).
Thanks!!

(If it’s relevant, I’m loading the fsaverage orig.mgz and aseg.mgz into 
freeview and loading my ColorLUT table onto the aseg.mgz there, because I can’t 
figure out how to get this working in tkmedit).

Best,
Stephanie

Stephanie N. DeCross
Clinical Research Coordinator
Psychiatric Neuroimaging Research Program
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, Rm 2620A
Charlestown, MA 02129
Phone: (617) 724-3283
Fax: (617) 726-4078




#$Id:   FreeSurferColorLUT.txt,v1.70.2.72012/08/27  
17:20:08nicks   Exp $   

#No.Label   Name:   R   G   B   A   

0   Unknown 0   0   0   255 
1   Left-Cerebral-Exterior  0   0   0   255 

2   Left-Cerebral-White-Matter  0   0   0   255 

3   Left-Cerebral-Cortex0   0   0   255 

4   Left-Lateral-Ventricle  0   0   0   255 

5   Left-Inf-Lat-Vent   0   0   0   255 

6   Left-Cerebellum-Exterior0   0   0   255 

7   Left-Cerebellum-White-Matter0   0   0   255 

8   Left-Cerebellum-Cortex  0   0   0   255 

9   Left-Thalamus   0   0   0   255 
10  Left-Thalamus-Proper0   0   0   255 

11  Left-Caudate220 216 20  255 
12  Left-Putamen0   0   0   255 
13  Left-Pallidum   0   0   0   255 
14  3rd-Ventricle   0   0   0   255 
15  4th-Ventricle   0   0   0   255 
16  Brain-Stem  0   0   0   255 
17  Left-Hippocampus0   225 0   255 

18  Left-Amygdala   0   225 0   255 
19  Left-Insula 0   0   0   255 
20  Left-Operculum  0   0   0   255 
21  Line-1  0   0   0   255 
22  Line-2  0   0   0   255 
23  Line-3  0   0   0   255 
24  CSF 0   0   0   255 
25  Left-Lesion 0   0   0   255 
26  Left-Accumbens-area 0   0   0   255 

27  Left-Substancia-Nigra   0   0   0   255 

28  Left-VentralDC  0   0   0   255 
29  Left-undetermined   0   0   0   255 

30  Left-vessel 0   0   0   255 
31  Left-choroid-plexus 0   0   0   255 

32  Left-F3orb  0   0   0   255 
33  Left-lOg0   0   0   255 
34  Left-aOg0   0   0   255 
35  Left-mOg0   0   0   255 
36  Left-pOg0   0   0   255 
37  Left-Stellate   0   0   0   255 
38  Left-Porg   0   0   0   255  

Re: [Freesurfer] Volumetric measurments and difference between results from "recon_all" and "mri_segstats"

[Douglas N Greve]

see if this link answers your question

http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Whatgoesintothecalculationofsubcorticalvolume.3FWehavetriedaddingvolumesofindividualsubcorticalareasbutthetotaldoesnotequalthesubcorticalvolumeprovidedbyaseg.Isthesubcorticalvolumecalculationaccurate.3F

On 05/05/2016 11:59 AM, Saeed Mahdizadeh Bakhshmand wrote:
> Hello Folks,
>
>  I used the recon-all -i -all -segmentation for the structural 
> image. FreeSurfer makes several folder and one of them is "stats". In 
> this folder, there is aseg.stats that includes volume of different 
> brain regions. Also, I found "mri_segstats" command line that gives us 
> the volume of the same brain regions. But, there is significant 
> difference between reported numbers  from these two methods . I would 
> say the difference is approximately 200 mm3 for each brain region. Do 
> you know what is correct way to measure volume of segmented brain 
> regions using FreeSurfer?
>
> Cheers,
> Saeed
>
>
> ___
> 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: 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/

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Re: [Freesurfer] Cortical Parcellation

[Douglas N Greve]

To see whether the final label is correct, load the label in freeview or 
tksurfer and see if it looks right.

You can use mris_anatomical_stats to get the volumes, etc, from the 
label (-l option). You may want to recombine the lobes into an 
annotation with mris_label2annot

doug

On 05/05/2016 12:17 PM, Heidi Foo wrote:
> Dear FreeSurfer experts,
>
> I apologise for posting this again. I am unable to get the volumes for 
> the cortical regions despite following the commands on 
> https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
>
> I am using FS5.3 to do the parcellation.
>
> I created a folder called "labels" inside each of my subject folder. 
> Attached the output.
>
> I tried to use mri_mergelabels -i label1 -i label2 -o outputlabel. 
> Attached the command as well as the output.
> *I am not sure if the output is correct and also, how should I get the 
> total volume for each lobe out? *
> Thank you so much for your help.
> Regards,
> Heidi Foo
>
>
> ___
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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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] Resting-state fcMRI analysis with GLM

[Douglas N Greve]

I guess I'm unclear as to what you are trying to do. Are you trying to 
do a time series analysis of the resting state to extract, eg, 
correlation with a seed? Or have you already done your time series 
analysis on each subject, reducing each to a single number at each 
voxel, and now you are doing a group analysis?
doug

On 05/05/2016 11:44 AM, Eun Young Choi wrote:
> Thanks, Doug.
>
> I'm still a little unclear about how to set up a timeseries regressor 
> (120 timepoints) in the design matrix while also specifying the # of 
> subjects (500). Would the design matrix be a 500x120 or 120x500?
>
> I should mention that my ultimate goal is to find a statistically sig. 
> threshold for a cortical fcMRI map with 500 subjects. Traditional 
> correction for multiple comparisons, like Bonferroni and FDR, are not 
> sufficient. So I'd now like to find a cluster size-based correction 
> threshold using mri_glm-sim. Hence, my desire to create the cortical 
> fcMRI map using mri_glmfit, so I can get the files needed for 
> mri_glm-sim. Is this an okay approach, or is there a better way to do 
> this?
>
> Thank you so much,
> Eun Young
>
>
>
> On Wed, May 4, 2016 at 3:15 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> We don't usually use mri_glmfit for this kind of thing. If you want to
> do it this way, then you cannot use an FSGD file. Instead, create a
> design matrix with the seed time course then pass that to mri_glmfit
> with the --X option (and no --fsgd option).
>
> On 05/04/2016 10:17 AM, Eun Young Choi wrote:
> >
> > Hi all,
> >
> > I'd like to run a resting-state fcMRI analysis within the GLM
> > (mri_glmfit), but I'm not completely sure how to set this up in the
> > FSGD file. I've seen the online tutorial of age vs cortical
> thickness,
> > but I'm not sure how to specify a regressor with a timeseries. Does
> > anyone have an example of an FSGD file for this?
> >
> > Thanks!
> > Eun Young
> >
> >
> >
> > ___
> > 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: 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/
>
> ___
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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 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.
>
>
>
>
> -- 
>
> *Eun Young Choi, PhD*
>
> Post-doctoral Associate
>
> University of Rochester Medical Center
>
> 601 Elmwood Ave, Box 711
>
> Rochester, NY 14642
>
> cell: 551-580-1572
>
>
>
> ___
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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: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] does lGI needs correction for any global measure?

[Douglas N Greve]

On 05/02/2016 07:39 AM, maaike rive wrote:
> Dear freesurfer experts,
>  
>
>
>  
> I have a question regarding correction of cortical measures or global 
> measures (ICV, total surface area). As I understand from literature 
> and the freesurfer wiki, a model for thickness should not be corrected 
> for ICV (since thickness does not scale with total brain volume), but 
> surface area should be corrected since is does scale with total brain 
> volume. Three questions:
>
>  
>
>
>  
> 1. should I use ICV or should I use total surface area (TSA) as 
> covariate in the model to correct surface area (by the way, average 
> ICV and TSA do not differ between the groups to compare )?
>
>
Not sure. They will be different models. ICV should not change over the 
lifetime whereas total surface area will.
>  
> 2. does lGI also need correction? does it scale with volume? If so, do 
> I need to correct for ICV or for TSA? Usually I see no correction but 
> some do use ICV...
>
>
I don't know, perhaps Marie will weigh in
>  
> 3. even if the average of certain measures (like ICV/TSA, or gender, 
> or age) does not differ between groups, should they be added to the 
> model? If I do not correct for gender, for example, my results change 
> and most papers do use age and gender as covariates if they compare 
> groups despite a lack of differences between groups...
>
>
They can still reduce intersubject variance.
doug
>  
>
>
>  
> Thanks,
>
>  
>
>
>  
> Maaike
>
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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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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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Resting-state fcMRI analysis with GLM

[Eun Young Choi]

Hi Doug,

Sorry for the confusion. I currently have individual and group mean fcMRI
z-maps from a seed based resting-state analysis (non GLM), but I could also
do a GLM-involved analysis for each subject with the seed's timeseries as a
regressor. My ultimate goal is have a group z-map that is thresholded at
some statistically meaningful threshold. I've tried Bonferroni and FDR
corrections, but they're not stringent enough (i.e., even weak correlations
are highly significant). So I started looking into doing a cluster
size-based correction threshold, which brought me to mri_glmsim and
mri_glmfit. But if there's a way to threshold a group zmap without
mri_glmsim, I could do that.

Let me know if I can explain further. Thank you!
Eun Young


On Thu, May 5, 2016 at 12:22 PM, Douglas N Greve 
wrote:

> I guess I'm unclear as to what you are trying to do. Are you trying to
> do a time series analysis of the resting state to extract, eg,
> correlation with a seed? Or have you already done your time series
> analysis on each subject, reducing each to a single number at each
> voxel, and now you are doing a group analysis?
> doug
>
> On 05/05/2016 11:44 AM, Eun Young Choi wrote:
> > Thanks, Doug.
> >
> > I'm still a little unclear about how to set up a timeseries regressor
> > (120 timepoints) in the design matrix while also specifying the # of
> > subjects (500). Would the design matrix be a 500x120 or 120x500?
> >
> > I should mention that my ultimate goal is to find a statistically sig.
> > threshold for a cortical fcMRI map with 500 subjects. Traditional
> > correction for multiple comparisons, like Bonferroni and FDR, are not
> > sufficient. So I'd now like to find a cluster size-based correction
> > threshold using mri_glm-sim. Hence, my desire to create the cortical
> > fcMRI map using mri_glmfit, so I can get the files needed for
> > mri_glm-sim. Is this an okay approach, or is there a better way to do
> > this?
> >
> > Thank you so much,
> > Eun Young
> >
> >
> >
> > On Wed, May 4, 2016 at 3:15 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > We don't usually use mri_glmfit for this kind of thing. If you want
> to
> > do it this way, then you cannot use an FSGD file. Instead, create a
> > design matrix with the seed time course then pass that to mri_glmfit
> > with the --X option (and no --fsgd option).
> >
> > On 05/04/2016 10:17 AM, Eun Young Choi wrote:
> > >
> > > Hi all,
> > >
> > > I'd like to run a resting-state fcMRI analysis within the GLM
> > > (mri_glmfit), but I'm not completely sure how to set this up in the
> > > FSGD file. I've seen the online tutorial of age vs cortical
> > thickness,
> > > but I'm not sure how to specify a regressor with a timeseries. Does
> > > anyone have an example of an FSGD file for this?
> > >
> > > Thanks!
> > > Eun Young
> > >
> > >
> > >
> > > ___
> > > 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: 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  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.
> >
> >
> >
> >
> > --
> >
> > *Eun Young Choi, PhD*
> >
> > Post-doctoral Associate
> >
> > University of Rochester Medical Center
> >
> > 601 Elmwood Ave, Box 711
> >
> > Rochester, NY 14642
> >
> > cell: 551-580-1572
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Thanks for the quick reply.

Is there a difference  from qcache/mris_fwhm with mris_smooth and
mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
analysis?

Thanks,
Ajay

On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
wrote:

> Hi Freesurfer Experts,
>Just as a followup through my reading i've come across posts which use
> qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
> cortical thickness analysis I would like to smooth all of my
> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
> group analysis.  After finding regions of difference, I would then like to
> use the ROI to extract each individual's mean thickness in the ROI in order
> to run a correlation with other measures.  Based on this, I assume it would
> make sense to use smoothed data to identify the ROI and then use unsmoothed
> data for extracting actual thickness measures (does lh.thickness.fsaverage
> contain the original thickness or warped thickness values).
>
> I am unsure which smoothing is the most accurate or preferred.  In using
> qcache the smoothness of the images do not seem to reach the filter level
> (based on the earlier email) so I am not sure if there is a freesurfer tool
> to check the smoothness level or if the qcache smoothness levels make sense
> for cortical thickness.
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
> wrote:
>
>> Hi Freesurfer Experts,
>>I am trying to understand the difference between qcache option and
>> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
>> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
>> (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
>> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
>> and 20mm it was approximately 9.3-9.9 smoothness level.
>>
>> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
>> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
>> using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
>>
>>
>> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate
>> to use for a cortical thickness analysis.
>>
>> 2) For qdec if I select the 15mm  option does it assume the smoothness is
>> 15mm when calculating monte carlo corrections?  Would there be a different
>> way to estimate this since my smoothness at 15mm is closer to 10mm?
>>
>> Thanks,
>> Ajay
>>
>
>
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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas N Greve]

There is not a difference between mris_fwhm and mri_surf2surf. 
mris_smooth smoothes the xyz coordinates of the vertices of a surface 
(the others smooth an overlay).

On 05/05/2016 03:53 PM, Ajay Kurani wrote:
> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with mris_smooth and 
> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical 
> thickness analysis?
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani  > wrote:
>
> Hi Freesurfer Experts,
>Just as a followup through my reading i've come across posts
> which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for
> smoothing.  For my cortical thickness analysis I would like to
> smooth all of my rh/lh.thickness.fsaverage.mgh files for each
> subject in order to run a group analysis.  After finding regions
> of difference, I would then like to use the ROI to extract each
> individual's mean thickness in the ROI in order to run a
> correlation with other measures.  Based on this, I assume it would
> make sense to use smoothed data to identify the ROI and then use
> unsmoothed data for extracting actual thickness measures (does
> lh.thickness.fsaverage contain the original thickness or warped
> thickness values).
>
> I am unsure which smoothing is the most accurate or preferred.  In
> using qcache the smoothness of the images do not seem to reach the
> filter level (based on the earlier email) so I am not sure if
> there is a freesurfer tool to check the smoothness level or if the
> qcache smoothness levels make sense for cortical thickness.
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani
> mailto:dr.ajay.kur...@gmail.com>> wrote:
>
> Hi Freesurfer Experts,
>I am trying to understand the difference between qcache
> option and mris_fwhm and which is appropriate for a cortical
> thickness analysis.  I processed my  files with qcache and
> have lh.thickness.fsaverage.fwhm15.gii (converted) files.  I
> used an afni tool SurfFWHM to estimate the smoothness of a
> subject at when looking at the fwhm0 image it iwas 5.5 and for
> 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
>
> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only
> --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o
> test_15.gii  and when using SurfFWHM on the smae subject the
> smoothness was estimated at 11.25.
>
>
> 1) I am not sure if the qcache or the mris_fwhm file is more
> appropriate to use for a cortical thickness analysis.
>
> 2) For qdec if I select the 15mm  option does it assume the
> smoothness is 15mm when calculating monte carlo corrections? 
> Would there be a different way to estimate this since my
> smoothness at 15mm is closer to 10mm?
>
> Thanks,
> Ajay
>
>
>
>
>
> ___
> 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: 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/

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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Thanks for the clarification.  So in the case of cortical thickness,
qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
should be getting similar results if everything is entered in the same
fashion.  This would be the approriate choice compared to mri_smooth.

For mri_surf2surf I used the following command for smoothing LGI and
cortical thickness and converting to .gii files.

mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
mris_convert -c rh.thickness.fwhm15.mgz
$FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii


1) For cortical thickness does it make sense to use the --cortex option or
should I specify a mask of some type (if so which) in mris_surf2surf?

2) For converting files to .gii should I be using rh.white as the option or
should it be rh.pial?


Best,
Ajay



On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
wrote:

> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with mris_smooth and
> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
> analysis?
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
> wrote:
>
>> Hi Freesurfer Experts,
>>Just as a followup through my reading i've come across posts which use
>> qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
>> cortical thickness analysis I would like to smooth all of my
>> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
>> group analysis.  After finding regions of difference, I would then like to
>> use the ROI to extract each individual's mean thickness in the ROI in order
>> to run a correlation with other measures.  Based on this, I assume it would
>> make sense to use smoothed data to identify the ROI and then use unsmoothed
>> data for extracting actual thickness measures (does lh.thickness.fsaverage
>> contain the original thickness or warped thickness values).
>>
>> I am unsure which smoothing is the most accurate or preferred.  In using
>> qcache the smoothness of the images do not seem to reach the filter level
>> (based on the earlier email) so I am not sure if there is a freesurfer tool
>> to check the smoothness level or if the qcache smoothness levels make sense
>> for cortical thickness.
>>
>> Thanks,
>> Ajay
>>
>> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
>> wrote:
>>
>>> Hi Freesurfer Experts,
>>>I am trying to understand the difference between qcache option and
>>> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
>>> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
>>> (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
>>> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
>>> and 20mm it was approximately 9.3-9.9 smoothness level.
>>>
>>> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
>>> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
>>> using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
>>>
>>>
>>> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate
>>> to use for a cortical thickness analysis.
>>>
>>> 2) For qdec if I select the 15mm  option does it assume the smoothness
>>> is 15mm when calculating monte carlo corrections?  Would there be a
>>> different way to estimate this since my smoothness at 15mm is closer to
>>> 10mm?
>>>
>>> Thanks,
>>> Ajay
>>>
>>
>>
>
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Re: [Freesurfer] Correcting defect

[Katarina Trojacanec]

Hi Bruce,

I uploaded the subject dirs (base for TP1_4 and TP2_4, as well as the 
cross-sectionally processed time points for TP1, TP2, and TP4). In the 
meantime, one of them, template TP1_4 has finished with error. The other one 
(base TP2_4) is still running.

What do you suggest in this situation.

Sorry for the inconvenience.

Cheers.

Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Thursday, May 5, 2016 4:20:31 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correcting defect

Hi Katarina

if you want us to look you need to upload the entire subject dirs (tarred
and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D
mode and just see what the big defects look like. If you load the
orig.nofix at the same time you can goto a vertex in the big defect you see
on the inflated by typing its index into the info winwo for the orig.nofix.
This will be automated in v6

Bruce


On Thu, 5 May 2016, Katarina Trojacanec wrote:

> Thank you.
> I have uploaded the files (lh.inflated_TP_1_4.nofix and 
> lh.inflated_TP_2_4.nofix).
>
> What should I do as a next step?
>
> Cheers
> Katarina Trojacanec, M.Sc.
> Teaching and research assistant
>
> Faculty of Computer Science and Engineering
> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: Wednesday, May 4, 2016 2:35 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Correcting defect
>
> sure. Or you can load the ?h.inflated.nofix and look at it - it should be
> obvious if there is a huge defect (you can also load the file
> ?h.defect_labels as an overlay on that surface and it will show you the
> segmentation of the defects)
>
> cheers
> Bruce
> On Wed, 4 May 2016, Katarina Trojacanec wrote:
>
>>
>> Dear FreeSurfer Team,
>>
>>
>> I have been trying to run creation of template with FreeSurfer. However,
>> for two cases for one patient (case 1: template based on TP1 and TP4, case
>> 2: template based on TP2 and TP4), the correcting defect step is running
>> too long. According to the information in the mail archive, the defects are
>> probably too big, and that is the reason for the long processing.
>>
>>
>> May I send you via ftp the subjects directories so you can help me to
>> proceed with this subject, because I am not able to figure out and correct
>> the problem? Should I send you the base directories in their current state
>> or the cross-sectionally processed time points as well?
>>
>>
>> Best Regards,
>>
>>
>> Katarina Trojacanec, M.Sc.
>> Teaching and research assistant
>>
>> Faculty of Computer Science and Engineering
>> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
>>
>>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] patient case study at two time points

[Zeng, Qi]

Hi All,

I was running freesurfer for a patient case of two time points. Will you
suggest to run it as a group, such as one time point as a template and
followed by longitudinal study, discussing atrophy or run these two time
points separately as two individual, running everything such recon-all,
dt-recon twice and comparing the result, such as thickness, volume and FA?
BTW, I post a question about FA display before: will anything lead to a
rectangular FA display, with extra diffusion out of the brain skull (no
errors during recon and dt …)?

Best,
Qi
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[Freesurfer] glmfit --table (by tract TRACULA outputs)

[Pedro Rosa]

Dear list,
I am trying to use mri_glmfit to run statistics on TRACULA outputs (by
tract), as suggested by the wiki (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics).
I used the following command line:

mri_glmfit --glmdir ilf.glmdir --table ilf.txt --fsgd sociodemo.fsgd --C
2G1V-1100.mtx

It ends without errors.

How should I proceed with correction for multiple comparisons, as I cannot
use Monte Carlo?

Best,

Pedro.
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Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Bronwyn Overs]

Hi Doug,

I tried to run the mri_surf2surf command as follows and got this error:

[b.overs~]$ mri_surf2surf --srcsubject fsaverage --srcsurfval 
lh.Yeo2011_7Networks_N1000.annot --trgsubject testsubj --trgsurfval 
lh.Yeo2011_7Networks_N1000.annot --hemi lh --save-annot

ERROR: Option --save-annot unknown
[b.overs~]$

I could not see any --save annot option in the help file. I am running 
this correctly? Should I be suing the .mgz file as the input or is the 
annotation file ok as this is what I want to resample?


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


On 6/05/2016 12:24 am, Douglas Greve wrote:



On 5/4/16 11:40 PM, Bronwyn Overs wrote:

Hi Freesurfer Mailing List,

I wish to extract stats for my sample for the Yeo 2011 cortical 
parcellations and the Choi 2012 striatal parcellations (7 networks) 
that are provided for download on the freesurfer wiki. My questions 
are as follows:


1. I noticed that the Yeo 2011 annot files are already available in 
fsaverage/label. How do I map these annot file to each of my subjects 
so that I can extract stats?

Use mri_surf2surf with the --save-annot option
2. For the Choi 2012 files I wish to use 
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . 
How do I map this file to each of my subjects so that I can extract 
stats for the 7Network parcellation?

I don't know about this file. Where is it? Is it something we distribute?
doug


--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to 
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