Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points

[Ed Gronenschild]

Hi Bruce,

I'm confused about this.
The manual-intervention workflow directives listed in recon-all (6 beta)
tell that the series of commands should be:
-autorecon2
-autorecon2-cp
-autorecon3

-autorecon2 processes stages 6-23
and
-autorecon2-cp process stages 12-23

So it seems to be a waste of time to process stages 12-23 twice.

My question is: how to run stages 6-23 with control points?

Cheers,
Ed

On 26 Feb 2016, at 14:13,   
 wrote:



Hi Ed

if you run the skull stripping the autorecon2 and autorecon3 it should
detect and preserve your manual interventions

cheers
Bruce


On Thu, 25 Feb 2016, Gronenschild Ed (NP) wrote:


Hi,

I have made some manual skullstrip adjustments and added a
number of control points in the white matter.
How should I proceed with recon-all to incorporate both adjustments?

Cheers,
Ed

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Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points

[Bruce Fischl]

Hi Ed

just run them once - it will detect the manual interventions and preserve 
them.


cheers
Bruce
On Mon, 29 Feb 2016, Ed Gronenschild wrote:


Hi Bruce,
I'm confused about this.
The manual-intervention workflow directives listed in recon-all (6 beta)
tell that the series of commands should be:
-autorecon2
-autorecon2-cp
-autorecon3

-autorecon2 processes stages 6-23
and
-autorecon2-cp process stages 12-23

So it seems to be a waste of time to process stages 12-23 twice.

My question is: how to run stages 6-23 with control points?

Cheers,
Ed

On 26 Feb 2016, at 14:13, 
 wrote:

  Hi Ed

if you run the skull stripping the autorecon2 and autorecon3 it
should 
detect and preserve your manual interventions

cheers
Bruce


On Thu, 25 Feb 2016, Gronenschild Ed (NP) wrote:

  Hi,

I have made some manual skullstrip adjustments and added a
number of control points in the white matter.
How should I proceed with recon-all to incorporate both
adjustments?

Cheers,
Ed

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Re: [Freesurfer] number of vertices

[Bruce Fischl]

Hi Daniel

the number of vertices will vary depending on the surface area and geometry 
of the white matter for each hemisphere.


cheers
Bruce


On Mon, 29 Feb 2016, Yang, Daniel wrote:


Dear FreeSurfer experts,

Can you please indicate the number of vertices FreeSurfer use in each 
hemisphere to reconstruct the brain (e.g., cortical
thickness)? Is there a fixed number or an approx. number?

Many thanks,
Daniel

-- 
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Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu

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Re: [Freesurfer] number of vertices

[Yang, Daniel]

Hi Bruce,

Is it okay to say that it is approximately 160,000 vertices per
hemisphere? I found the answer from a paper
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824100/pdf/fnhum-07-00722.pdf
).

Best,
Daniel

-- 
Daniel Yang, Ph.D.
Yale Child Study Center

E-mail: daniel.yj.y...@yale.edu




On 2/29/16, 11:42 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

>Hi Daniel
>
>the number of vertices will vary depending on the surface area and
>geometry 
>of the white matter for each hemisphere.
>
>cheers
>Bruce
>
>
>On Mon, 29 Feb 2016, Yang, Daniel wrote:
>
>> Dear FreeSurfer experts,
>> 
>> Can you please indicate the number of vertices FreeSurfer use in each
>>hemisphere to reconstruct the brain (e.g., cortical
>> thickness)? Is there a fixed number or an approx. number?
>> 
>> Many thanks,
>> Daniel
>> 
>> -- 
>> Daniel Yang, Ph.D.
>> Yale Child Study Center
>> E-mail: daniel.yj.y...@yale.edu
>> 


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[Freesurfer] number of vertices

[Yang, Daniel]

Dear FreeSurfer experts,

Can you please indicate the number of vertices FreeSurfer use in each 
hemisphere to reconstruct the brain (e.g., cortical thickness)? Is there a 
fixed number or an approx. number?

Many thanks,
Daniel

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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Re: [Freesurfer] number of vertices

[Bruce Fischl]

it's usually a bit less than that - aroudn 140K or so
Bruce

On Mon, 29 Feb 2016, 
Yang, Daniel wrote:

> Hi Bruce,
>
> Is it okay to say that it is approximately 160,000 vertices per
> hemisphere? I found the answer from a paper
> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824100/pdf/fnhum-07-00722.pdf
> ).
>
> Best,
> Daniel
>
>
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Re: [Freesurfer] number of vertices

[Yang, Daniel]

Thanks! That number helps. Just want to get an approx. number in general.

Best,
Daniel

-- 
Daniel Yang, Ph.D.
Yale Child Study Center

E-mail: daniel.yj.y...@yale.edu




On 2/29/16, 11:52 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

>it's usually a bit less than that - aroudn 140K or so
>Bruce
>
>On Mon, 29 Feb 2016,
>Yang, Daniel wrote:
>
>> Hi Bruce,
>>
>> Is it okay to say that it is approximately 160,000 vertices per
>> hemisphere? I found the answer from a paper
>> 
>>(https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ncbi.nlm.nih.gov
>>_pmc_articles_PMC3824100_pdf_fnhum-2D07-2D00722.pdf&d=AwIBAg&c=-dg2m7zWuu
>>DZ0MUcV7Sdqw&r=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=z_5IoiYhMwET
>>NcHWHhQzvAvNmllYCkZY02MMWkBOj_A&s=0bpC-Abjox4A5ZgIdt-inwG08b5S26qYBdABg43
>>hTTo&e= 
>> ).
>>
>> Best,
>> Daniel
>>
>>
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[Freesurfer] Patch for ribbon.mgz failure

[Philip Deming]

Freesurfer community,


I'd like to repost a question I asked last week, regarding a failure to create 
the ribbon.mgz file in -autorecon2. The release notes for 5.3 indicate a patch 
should fix this:


Creation of the aseg.stats table fails when only running -autorecon1 or 
-autorecon2 because ribbon.mgz is not present. This has been fixed. Ask for a 
patch.


Can someone please instruct on how to obtain this patch?


Thanks!

Phil



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Philip Deming 

Sent: Wednesday, February 24, 2016 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Patch for ribbon.mgz failure


Hi Freesurfer team,


I'm having an issue running -autorecon2. The program exits with errors because 
it is unable to create the ribbon.mgz file. According to the version 5.3 
release notes, there is a patch available to fix this issue:


Creation of the aseg.stats table fails when only running -autorecon1 or 
-autorecon2 because ribbon.mgz is not present. This has been fixed. Ask for a 
patch.


How can I obtain the patch to fix the ribbon.mgz issue?


Thanks,

Phil
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[Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Hi Freesurfer experts,

I have created an annotation file by several label files using
mris_label2annot command in Freesurfer. The problem is that when I open
this annot file in tksurfer and click on colored regions which corresponded
to specific labels I had chosen them, I do not have their name on the
vertex information part at the bottom of tksurfer GUI. It shows very
different names for these regions. May you explains me what is the problem
I could not see the exact region's name as I have them for label files?

Thanks,
Faezeh Vedaei
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faeze,

I believe the name comes from the Color LUT file. Try changing the
name in there.

hth
d

On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei  wrote:
> Hi Freesurfer experts,
>
> I have created an annotation file by several label files using
> mris_label2annot command in Freesurfer. The problem is that when I open this
> annot file in tksurfer and click on colored regions which corresponded to
> specific labels I had chosen them, I do not have their name on the vertex
> information part at the bottom of tksurfer GUI. It shows very different
> names for these regions. May you explains me what is the problem I could not
> see the exact region's name as I have them for label files?
>
> Thanks,
> Faezeh Vedaei
>
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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[Freesurfer] Doubts with Longitudinal Analysis Repeated Measures ANOVA

[Universidad de Deusto]

Dear FS Experts,

I'm interested in performing Repeated Measures ANOVA 2x2. I have 2 groups
and two times (pre and post treatment).
I have checked the tutorial for repeated measures anova and previous emails:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg45703.HTML
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg45650.HTML

However, it is not clear to me, which steps I have to follow to create the
matrix and obtain the results for groupxtime effect.

I would be very grateful if someone could help me with this analysis,

Thank you in advance,

Best Regards
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Douglas N Greve]

try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize


On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
> I changed the directory and it ran, but with errors. I had to change 
> the last part --surf lh.seghead --surf-smooth 10 because it does not 
> recognise --surf. When I change this to --o, it runs but with errors.
>
> On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
>
> On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
>> It seems to be giving me an error and saying it cannot read the
>> seghead.mgz file.
> Is it in the same directory where you are running the command? If
> so, what is the terminal output?
>>
>> From my earlier question; do you know how to check if lh.seghead
>> is corrupted?
> If you can view it in tksurfer/freeview, then it is probably not
> corrupted. I vaguely remember that there was some problem reading
> this file in matlab, but I don't remember every coming up with a fix
>
>>
>> On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> you can try
>>
>> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead
>> --surf-smooth 10
>>
>>
>>
>>
>> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
>>> Is it possible to use a different function? Can I use
>>> mri_vol2surf on the seghead.mgz file? Or do you think that
>>> mkheadsurf is the right one to be using?
>>>
>>> Thanks!!
>>>
>>> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve
>>> >> > wrote:
>>>
>>> Can you load it in tksurfer or freeview?
>>>
>>>
>>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
 Hi FreeSurfer users,

 I have used the "mkheadsurf" command to create a head
 surface for my subject. However when I try to use
 "read_surf" to read the "lh.seghead" file that is
 created, the magic number is not one that is recognised.

 Having read some previous posts/questions with similar
 problem/error, I think the problem is probably within
 the "lh.seghead" file. I think someone wrote that
 incompatibility of the magic number means that the
 surface is corrupted. Is there a way to check errors of
 mkheadsurf? Or whether something is wrong? It looked
 fine in freeview.

 Does anybody have any advice?

 Thanks,

 Maheen


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>>>
>>>
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>>>
>>>
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>>
>>
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>>   

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Hi,

Thank you for your response. Yes, you are right. The names come from the
color LUT file. But, the issue is that I chose the label files from that
LUT file too. It meas the source that I chose the label files from and the
source of the region's names in tksurfer are the same. The problem is just
I do not have the label's names I merged to create annot file, in the
tksurfer GUI. It shows another names of that list! So, what do you think
about? What is the problem?

Regards,
Faezeh Vedaei

On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
wrote:

> Hi Freesurfer experts,
>
> I have created an annotation file by several label files using
> mris_label2annot command in Freesurfer. The problem is that when I open
> this annot file in tksurfer and click on colored regions which corresponded
> to specific labels I had chosen them, I do not have their name on the
> vertex information part at the bottom of tksurfer GUI. It shows very
> different names for these regions. May you explains me what is the problem
> I could not see the exact region's name as I have them for label files?
>
> Thanks,
> Faezeh Vedaei
>
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Re: [Freesurfer] Patch for ribbon.mgz failure

[Douglas N Greve]

try copying this to $FREESURFER_HOME/bin
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats

On 02/24/2016 01:21 PM, Philip Deming wrote:
>
> Hi Freesurfer team,
>
>
> I'm having an issue running -autorecon2. The program exits with errors 
> because it is unable to create the ribbon.mgz file. According to the 
> version 5.3 release notes, there is a patch available to fix this issue:
>
>
> Creation of the aseg.stats table fails when only running -autorecon1 
> or -autorecon2 because ribbon.mgz is not present. This has been fixed. 
> Ask for a patch.
>
>
> How can I obtain the patch to fix the ribbon.mgz issue?
>
>
> Thanks,
>
> Phil
>
>
>
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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
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] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faeze,

It is difficult to help without more details, but in my experience,
(exact command, the color lut file in text in the email and what the
error in the naming was, which label went to which entry in the color
lut.)

You need to put the labels in the order of your custom color lut file.

hth
d

On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei  wrote:
> Hi,
>
> Thank you for your response. Yes, you are right. The names come from the
> color LUT file. But, the issue is that I chose the label files from that LUT
> file too. It meas the source that I chose the label files from and the
> source of the region's names in tksurfer are the same. The problem is just I
> do not have the label's names I merged to create annot file, in the tksurfer
> GUI. It shows another names of that list! So, what do you think about? What
> is the problem?
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
> wrote:
>>
>> Hi Freesurfer experts,
>>
>> I have created an annotation file by several label files using
>> mris_label2annot command in Freesurfer. The problem is that when I open this
>> annot file in tksurfer and click on colored regions which corresponded to
>> specific labels I had chosen them, I do not have their name on the vertex
>> information part at the bottom of tksurfer GUI. It shows very different
>> names for these regions. May you explains me what is the problem I could not
>> see the exact region's name as I have them for label files?
>>
>> Thanks,
>> Faezeh Vedaei
>
>
>
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[Freesurfer] Using N3 MNI and N3 FS corrections

[Adam Martersteck]

Hi Freesurfer users,

I have a question about using the N3 algorithm twice for processing ADNI
data:

Is it okay for data to have undergone the ADNI N3 correction (Boyes et al.
2008 http://www.ncbi.nlm.nih.gov/pubmed/18063391) AND then pushed through
the Freesurfer pipeline and undergo FS N3 correction (Zheng, Chee, and
Zagorodnov 2009 http://www.ncbi.nlm.nih.gov/pubmed/19559796)?

The problem stems from the fact that recent ADNI data has either undergone
gradient warping correction (http://www.ncbi.nlm.nih.gov/pubmed/16300968)
AND N3 correction or no corrections at all. The optimal solution would to
have just been able to download the grad warp’d data and push that through.


Thanks for any thoughts!
Adam
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Re: [Freesurfer] Using N3 MNI and N3 FS corrections

[Bruce Fischl]

Hi Adam

I don't think we know. It's probably ok, but you'll just have to try it 
out


Bruce
On Mon, 29 Feb 2016, Adam Martersteck wrote:


Hi Freesurfer users,

I have a question about using the N3 algorithm twice for processing ADNI
data:

Is it okay for data to have undergone the ADNI N3 correction (Boyes et al.
2008 http://www.ncbi.nlm.nih.gov/pubmed/18063391) AND then pushed through
the Freesurfer pipeline and undergo FS N3 correction (Zheng, Chee, and
Zagorodnov 2009 http://www.ncbi.nlm.nih.gov/pubmed/19559796)?

The problem stems from the fact that recent ADNI data has either undergone
gradient warping correction (http://www.ncbi.nlm.nih.gov/pubmed/16300968)
AND N3 correction or no corrections at all. The optimal solution would to
have just been able to download the grad warp’d data and push that through.

 
Thanks for any thoughts!
Adam

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[Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

[John Plass]

Hello Freesurfer Experts,
I wrote in recently about my parcellation troubles with an ex-vivo scan (
link
).
Digging further, I've found that the surfaces I've produced following
the Ex-Vivo
recon instructions 
are oriented properly when viewed in freeview (freeview -v mri/orig.mgz -f
surf/rh.white:edgecolor=blue surf/rh.pial:edgecolor=red), but are
misoriented in tkmedit (tkmedit $SUBID orig.mgz rh.white). I suspect that
something related this might be the source of the parcellation problems.
Any idea why this might be and how I can fix it?

Relevant background information:
*volumes were reoriented before FS processing using the command
"mri_convert -c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz
mprage.mgz"
*running freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 on Ubuntu 14.04

As always, I'm very grateful for any help you can provide.

John
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Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

[Bruce Fischl]

Hi John

when you say that they are oriented correctly in freeview, does that mean 
that they just overlay properly on the volume? Or that e.g. what freeview 
thinks is anterior is actually anterior, etc...?


cheers
Bruce


On Mon, 29 Feb 2016, John 
Plass wrote:



Hello Freesurfer Experts,
I wrote in recently about my parcellation troubles with an ex-vivo scan
(link). Digging further, I've found that the surfaces I've produced
following the Ex-Vivo recon instructions are oriented properly when viewed
in freeview (freeview -v mri/orig.mgz -f surf/rh.white:edgecolor=blue
surf/rh.pial:edgecolor=red), but are misoriented in tkmedit (tkmedit $SUBID
orig.mgz rh.white). I suspect that something related this might be the
source of the parcellation problems. Any idea why this might be and how I
can fix it?

Relevant background information:
*volumes were reoriented before FS processing using the command "mri_convert
-c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz  mprage.mgz"
*running freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 on Ubuntu 14.04

As always, I'm very grateful for any help you can provide.

John



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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Hi,

I checked again to arrange the labels in the order of LUT file, but the
result has not changed. Can you help me more how I can fix this problem?
Thank you so much for your time and help.

Regards,
Faezeh Vedaei

On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei  wrote:

> Hi,
>
> Thank you for your response. Yes, you are right. The names come from the
> color LUT file. But, the issue is that I chose the label files from that
> LUT file too. It meas the source that I chose the label files from and the
> source of the region's names in tksurfer are the same. The problem is just
> I do not have the label's names I merged to create annot file, in the
> tksurfer GUI. It shows another names of that list! So, what do you think
> about? What is the problem?
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
> wrote:
>
>> Hi Freesurfer experts,
>>
>> I have created an annotation file by several label files using
>> mris_label2annot command in Freesurfer. The problem is that when I open
>> this annot file in tksurfer and click on colored regions which corresponded
>> to specific labels I had chosen them, I do not have their name on the
>> vertex information part at the bottom of tksurfer GUI. It shows very
>> different names for these regions. May you explains me what is the problem
>> I could not see the exact region's name as I have them for label files?
>>
>> Thanks,
>> Faezeh Vedaei
>>
>
>
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faezeh,

Please provide more details (those i described in the earlier email).

Thanks
d

On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei  wrote:
> Hi,
>
> I checked again to arrange the labels in the order of LUT file, but the
> result has not changed. Can you help me more how I can fix this problem?
> Thank you so much for your time and help.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> Thank you for your response. Yes, you are right. The names come from the
>> color LUT file. But, the issue is that I chose the label files from that LUT
>> file too. It meas the source that I chose the label files from and the
>> source of the region's names in tksurfer are the same. The problem is just I
>> do not have the label's names I merged to create annot file, in the tksurfer
>> GUI. It shows another names of that list! So, what do you think about? What
>> is the problem?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi Freesurfer experts,
>>>
>>> I have created an annotation file by several label files using
>>> mris_label2annot command in Freesurfer. The problem is that when I open this
>>> annot file in tksurfer and click on colored regions which corresponded to
>>> specific labels I had chosen them, I do not have their name on the vertex
>>> information part at the bottom of tksurfer GUI. It shows very different
>>> names for these regions. May you explains me what is the problem I could not
>>> see the exact region's name as I have them for label files?
>>>
>>> Thanks,
>>> Faezeh Vedaei
>>
>>
>
>
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Hi

Thank you so much for your response. I attached here three files including
the command lines, LUT file , and the list of names I want to get and what
the result is actually. I'd appreciate if you look at them and let me know
what is wrong with that.

Regards,
Faezeh Vedaei

On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei  wrote:

> Hi,
>
> I checked again to arrange the labels in the order of LUT file, but the
> result has not changed. Can you help me more how I can fix this problem?
> Thank you so much for your time and help.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> Thank you for your response. Yes, you are right. The names come from the
>> color LUT file. But, the issue is that I chose the label files from that
>> LUT file too. It meas the source that I chose the label files from and the
>> source of the region's names in tksurfer are the same. The problem is just
>> I do not have the label's names I merged to create annot file, in the
>> tksurfer GUI. It shows another names of that list! So, what do you think
>> about? What is the problem?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi Freesurfer experts,
>>>
>>> I have created an annotation file by several label files using
>>> mris_label2annot command in Freesurfer. The problem is that when I open
>>> this annot file in tksurfer and click on colored regions which corresponded
>>> to specific labels I had chosen them, I do not have their name on the
>>> vertex information part at the bottom of tksurfer GUI. It shows very
>>> different names for these regions. May you explains me what is the problem
>>> I could not see the exact region's name as I have them for label files?
>>>
>>> Thanks,
>>> Faezeh Vedaei
>>>
>>
>>
>


mris_label2annot.docx
Description: MS-Word 2007 document


LUT file (ctab).xlsx
Description: MS-Excel 2007 spreadsheet


label's name.docx
Description: MS-Word 2007 document
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faezeh,

Can you send these in the text of the email. It is very hard to deal
with these files? The LUT file shouldn't be an excel file it should be
a plain text document (please attach).

Thanks,
D

On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei  wrote:
> Hi
>
> Thank you so much for your response. I attached here three files including
> the command lines, LUT file , and the list of names I want to get and what
> the result is actually. I'd appreciate if you look at them and let me know
> what is wrong with that.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> I checked again to arrange the labels in the order of LUT file, but the
>> result has not changed. Can you help me more how I can fix this problem?
>> Thank you so much for your time and help.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> Thank you for your response. Yes, you are right. The names come from the
>>> color LUT file. But, the issue is that I chose the label files from that LUT
>>> file too. It meas the source that I chose the label files from and the
>>> source of the region's names in tksurfer are the same. The problem is just I
>>> do not have the label's names I merged to create annot file, in the tksurfer
>>> GUI. It shows another names of that list! So, what do you think about? What
>>> is the problem?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
>>> wrote:

 Hi Freesurfer experts,

 I have created an annotation file by several label files using
 mris_label2annot command in Freesurfer. The problem is that when I open 
 this
 annot file in tksurfer and click on colored regions which corresponded to
 specific labels I had chosen them, I do not have their name on the vertex
 information part at the bottom of tksurfer GUI. It shows very different
 names for these regions. May you explains me what is the problem I could 
 not
 see the exact region's name as I have them for label files?

 Thanks,
 Faezeh Vedaei
>>>
>>>
>>
>
>
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[Freesurfer] AAL atlas question

[pfotiad]

Hi FS community,

I have recon-ed a set of subjects and I was interested in also obtaining
structural info (cortical thickness, gray matter volume, surface area
etc.) based on a different atlas than the ones FS is using, and in
particular the AAL atlas.

I was wondering whether my approach would be the correct one or whether
there is another (better and more accurate) approach:

1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI
space into the native subjects' space,
2) Use mris_anatomical_stats to calculate the structural stats

Sorry for the potentially trivial question, and thank you for your time!

Best,
Panos

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[Freesurfer] question about white matter segmentation

[Jasmin Alves]

Hello freesurfer support,

I have been quality checking after the recon-all command according to the
trouble shooting tutorials and have noticed quite a few participants that
have white matter segmentation occurring on parts of the skull (see screen
shot) but these regions are not outlined as white matter, is it necessary
to use the voxel edit to remove where the skull is considered part of the
white matter mask?

Thank you,
Jasmin

-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Re: [Freesurfer] question about white matter segmentation

[Bruce Fischl]

nope, you don't have to worry about them if they are not grabbed by the 
surfaces.


cheers
Bruce
On Mon, 29 Feb 2016, Jasmin Alves wrote:


Hello freesurfer support,
I have been quality checking after the recon-all command according to the
trouble shooting tutorials and have noticed quite a few participants that
have white matter segmentation occurring on parts of the skull (see screen
shot) but these regions are not outlined as white matter, is it necessary to
use the voxel edit to remove where the skull is considered part of the white
matter mask?

Thank you,
Jasmin

--
Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 


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[Freesurfer] mysterious fsgd format error (not the end of line problem)

[Joseph Dien]

Hi,
   I’m having an fsgd error that has totally stumped me.  I’m trying to run the 
following command to compute the second level statistics:

mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz  --nii.gz 
--fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C normAcc.mtx

I get the error message:

Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white
gdfReadHeader: reading RPA-accGT.fsgd
FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title

I used the utility flip to make sure the file was in UNIX format (with 
linefeeds).
I then double-checked by reading in the binary codes with Matlab’s fread and 
directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed).

Here is the contents of the fsgd file.

GroupDescriptorFile 1
Title RP1
Class Main
Variables LogoAcc NormAcc OrthAcc PhonAcc
Input   RPA903  Main0.750.790.770.62
Input   RPA906  Main0.810.810.830.74
Input   RPA907  Main0.871   0.840.83
Input   RPA908  Main0.910.930.950.89
Input   RPA909  Main0.740.950.720.72
Input   RPA910  Main0.850.960.810.79
Input   RPA912  Main0.750.780.730.73
Input   RPA914  Main0.7 0.850.830.81
Input   RPA915  Main0.850.890.750.83
Input   RPA916  Main0.840.920.870.72
Input   RPA917  Main0.830.930.920.83
Input   RPA918  Main0.870.910.790.85
Input   RPA919  Main0.860.960.910.88
Input   RPA920  Main0.840.920.870.84
Input   RPA921  Main0.870.920.880.85
Input   RPA922  Main0.8 0.9 0.9 0.72

What’s really driving me to distraction is that a previous version of this file 
(with a different set of participants) works fine.  I’m attaching both.  
RPA-accGT.fsgd does not work and RPA-acc.fsgd does work.  Using Matlab’s fread, 
the first 85 characters (first four lines) of both files are identical.

I’m running on OS X 10.11.3.  I’m using FSFAST 5.20.  Matlab 2015b.

Any help would be greatly appreciated!

Joe



RPA-accGT.fsgd
Description: Binary data


RPA-acc.fsgd
Description: Binary data



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com

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Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

[John Plass]

Hi Bruce,
Thanks for your help. In freeview, the surface outline overlays on the
volume correctly, and both the volume and the surface are oriented
correctly in terms of R-L, A-P, and S-I axes. In tkmedit, the volume is
oriented correctly, but the surface appears to be oriented with some of the
axes swapped. E.g., from the coronal view in tkmedit, I see a coronal slice
of the volume, but the outline of an axial slice of the surface, with the
anterior part pointing down.

John
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[Freesurfer] Neurohackweek: a summer school for neuroimaging and data science, September 5th-9th 2016

[Ariel Rokem]

We are happy to announce a call for applications to participate in the
first installment of the Neurohackweek summer school for neuroimaging and
data science.

This 5 day hands-on workshop, held at the University of Washington eScience
Institute in Seattle, will focus on technologies used to analyze human
neuroimaging data, on methods used to extract information from large
datasets of publicly available data (such as the Human Connectome Project,
Open fMRI, etc.), and on tools for making neuroimaging research open and
reproducible.

Morning sessions will be devoted to lectures and tutorials, and afternoon
sessions will be devoted to participant-directed activities: guided work on
team projects, hackathon sessions, and breakout sessions on topics of
interest.


For more details, see: http://neurohackweek.github.io/

We are now accepting applications from researchers in different stages of
their career (graduate students, postdocs, faculty, and research
scientists) to participate at:
http://escience.washington.edu/neurohackweek2016-application

Accepted applicants will be asked to pay a fee of $200 upon final
registration. This fee will include participation in the course,
accommodation in the UW dorms, and two meals a day (breakfast and lunch),
for the duration of the course. A limited number of fee waivers and travel
grants will be available. We encourage students with financial need and
students from groups that are underrepresented in neuroimaging and data
science to apply for these grants (email applications to: aro...@uw.edu)

Important dates:

April 18th: Deadline for applications to participate

May 6th: Notification of acceptance

June 1st: Final registration deadline

On behalf of the instructors,

Ariel Rokem, UW eScience

Tal Yarkoni, UT Austin
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[Freesurfer] How to find the difference between to different fMRI datasets?

[Silas]

Dear FreeSurfer team,


Thank you for all your help so far!


I would like to visualize the difference between two fMRI data sets.

Data set1: Cortical activation during movement of a finger.

Data set2: Cortical activation during movement of a finger different from the 
first finger.


How can i perform this operation?


Best, Silas
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.