date:20160302

[Freesurfer] conflicting Monte Carlo simulation results...

2016-03-02 Thread Karl Liu

Dear Freesurfer experts:

I ran into a confusing problem when applying Monte Carlo
simulation to control for multiple comparisons. I am using the buckner data
from tutorial dataset.

I first tried the simulation based on Freesurfer;s 2012
manual:
(http://www.freesurfer.net/pub/docs/tarballs_for_courses/FreeSurferTutorial-2012.pdf)

mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z
5 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite

This produced a "mc-z.negative.sig.cluster.summary".
In this text, no clusters survived correction.

Later on, I applied on a slightly different script, based on
Freesurfer tutorial
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons)

mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4
neg \ --cwp 0.05\ --2spaces

It produced a "cache.th40.neg.sig.cluster.summary"
this time. But according to this result, 22 clusters survived.

Now I am quite confused, because both corrections have the
same voxel-wise (p=0.001) and cluster-wise (p=0.05) threshold. Where the drastic
discrepancies come from and which result is more reliable?

Many
thinks in advance.

Best,

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

2016-03-02 Thread Faeze Vedaei

Hi

Thank you so much for your help. I just got your meaning. I created new LUT
file by just changing randomly the RBG values for each 13 specific regions
and opened the annot file in tksurfer. And the strange issue is that just
for paracentral I used your values I had paracentral in tksurfer GUI name,
but for the rest of the regions I saw that problem I had before! (the
region's names were not the names in .ctab file). So, what do you think
about?

Regards,
Faeze

On Wed, Mar 2, 2016 at 2:59 PM, Faeze Vedaei  wrote:

> Hi,
>
> Thank you for your response. sorry, I could not understand what you mean.
> How you found 23 230 60 values for paracentral region? I mean. Are these
> from Freesurfer LUT?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei 
> wrote:
>
>> Thank you for your response. It is better to explain my question that the
>> coordinates for paracentral in .ctab file is '63 100 60', that you changed
>> these to '23 230 60' in your new version. My question is that how you
>> applied such this change on the RBG values for this region?
>>
>> Regards,
>> Faezeh
>>
>> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei 
>> wrote:
>>
>>> Thank you so much for you response. I should say that I know about what
>>> you are saying. My issue is that I have these 4 columns in my LUT file. Why
>>> and how can I change the numbers (RGB values) to create new LUT?
>>>
>>> Bests,
>>> Faezeh
>>>
>>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei 
>>> wrote:
>>>
 Hi,

 Thank you so much for you descriptions. I checked out the link you just
 sent me. Because I do not have many experiences working with Freesurfer, I
 really could not understand about how I can do such this revising in LUT
 file. Can you explain more about this? I truly appreciate your time and
 help.

 Regards,
 Faezeh Vedaei

 On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei 
 wrote:

> Hi,
>
> I really appreciate you for help me in this process. May you clarify
> me from which pattern you changed the RGB values for that region? How I 
> can
> change the coordinates for the others?
>
> Regards,
> Faezeh Vedaei
>
>
> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> I should let you know that, it works! It shows paracentral name in
>> tksurfer. So, how I have to revise my .ctab file to get the right result?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>> Thank you for your response. I just used the command you suggested
>>> to use by just a change in calling .ctab LUT file. I used the path:
>>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by 
>>> just
>>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file
>>> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
>>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
>>> opinion?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >> > wrote:
>>>
 Hi,


 Here is the text format of those files.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei <
 faezeved...@gmail.com> 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 <
> faezeved...@gmail.com> 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 <
>> faezeved...@gmail.com> 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.

Re: [Freesurfer] Topological White Matter Correction

2016-03-02 Thread Bruce Fischl


Hi Kiersten

the topology correction algorithm is this one:

http://www.ncbi.nlm.nih.gov/pubmed/11293693
cheers
Bruce

On Wed, 2 Mar 2016, Kiersten 
Snyder wrote:



Hello FreeSurfer Experts,What image processing technique is behind the
Topological White Matter Correction to correct topological defects? Is it
true that FreeSurfer take into account your edits as a "suggestion" and
incorporates into some type of algorithm?  I would like to have a more
thorough understanding of the image processing that this function utilizes.
Thanks for the help!
Kiersten

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Re: [Freesurfer] hippocampus subfields

2016-03-02 Thread Kanel, Prabesh

Sweet, just what I wanted.


Thank you,


Prabesh




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 

Sent: Wednesday, March 2, 2016 2:40 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampus subfields

OK now I get it ;-)
You can simply do:
mri_convert T2.FSspace.mgz T2.FSspace.resampled.mgz -odt float -rl 
[lr]h.hippoSfLabels-T1-T2.v10.mgz
The rl flag says: "reslice like the following volume"
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


From: "Prabesh Kanel" 
To: "Freesurfer support list" 
Sent: Wednesday, March 2, 2016 8:31:17 PM
Subject: Re: [Freesurfer] hippocampus subfields



Hi Eugenio,


Thank you, for your quick reply. It has happened to me in 4% of the cases, but 
my data sample is small like 100 data points.


Addition to the second question: When I segment the hippocampus, I get the 
discrete segmentation volume at 0.333 mm resolution in the file 
[lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each 
voxel is labelled based on the subfield. I can use mri_extract_label or 
mri_binarize to extract individual subfield. But this segmentation will have 
voxels with the original label. If I load the file along with the 
T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the 
intensities at this place, I believe the intensity value is from 
T2.FSspace.mgz. Are those intensities values different from the original T2 
images? If not, Is it possible to get those value at each voxel location?


Best Regards,

Prabesh


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 

Sent: Wednesday, March 2, 2016 12:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampus subfields

Hi Prabesh,
I think this is due to a bug that I found recently and which I'm trying to 
track down. Has it happened to you with many scans? The failure rate is less 
than 1% in my data.
Regarding your second question: I'm sure it's not too trivial ;-)  but I don't 
understand exactly what you mean. Do you want to deform the segmentations back 
to the original T2 space?
Cheers,
Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


From: "Prabesh Kanel" 
To: "Freesurfer support list" 
Sent: Wednesday, March 2, 2016 6:07:13 PM
Subject: [Freesurfer] hippocampus subfields


Freesurfer List,


I ran recon-all to segment hippocampus subfield using the development version 
of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and 
T2 images. But for some of the scans, the process stops at a point and doesn't 
seem to progress further.  That happens in only a few cases and only when the 
data are run using the flag -hippocampal-subfields-T1T2. I have attached a log 
file of one of the case in this email.

Another query that I have is to get T2 segmented subfields images (one with 
intensity values rather than labels). Is there an easier way to get T2 
subfields segmented images using the segmentation volumes and T2.FSspace.mgz. 
Sorry, if this question seems too trivial.

Regards,

Prabesh

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The information

[Freesurfer] Topological White Matter Correction

2016-03-02 Thread Kiersten Snyder

Hello FreeSurfer Experts,
What image processing technique is behind the Topological White Matter
Correction to correct topological defects? Is it true that FreeSurfer take
into account your edits as a "suggestion" and incorporates into some type
of algorithm?  I would like to have a more thorough understanding of the
image processing that this function utilizes.

Thanks for the help!
Kiersten
___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Unknown option DKTatlas40

2016-03-02 Thread Z K

It appears to be an issue with the dev build and should be fixed in 
tomorrows build.

-Zeke

On 03/02/2016 08:31 AM, Watson, Christopher wrote:
> The option should be:
> --annot aparc.DKTatlas40
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of marmaduke woodman 
> [marmaduke.wood...@univ-amu.fr]
> Sent: Wednesday, March 2, 2016 08:27
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Unknown option DKTatlas40
>
> hi
>
> I'm using the dev version of FreeSurfer on 64-bit Fedora 23.
>
>
> Recon-all runs fine but at the end I see
>
> $ recon-all -s tvb -aparc2aseg
> ...
>mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --DKTatlas40
>
> ERROR: Option --DKTatlas40 unknown
>
>
> Running that command
>
> $ mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos
>
> without the --DKTatlas40 appears to run correctly.
>
>
> Is this just an issue with the dev version or have I done something silly?
>
>
> thanks,
> Marmaduke
>
>
> ps bugr output
>
> FREESURFER_HOME: /opt/freesurfer
>
> Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160229
>
> RedHat release: Fedora release 23 (Twenty Three)
>
> Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

2016-03-02 Thread dgw

just change the values and re-run with different numbers and see what happens

On Wed, Mar 2, 2016 at 2:59 PM, Faeze Vedaei  wrote:
> Hi,
>
> Thank you for your response. sorry, I could not understand what you mean.
> How you found 23 230 60 values for paracentral region? I mean. Are these
> from Freesurfer LUT?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei  wrote:
>>
>> Thank you for your response. It is better to explain my question that the
>> coordinates for paracentral in .ctab file is '63 100 60', that you changed
>> these to '23 230 60' in your new version. My question is that how you
>> applied such this change on the RBG values for this region?
>>
>> Regards,
>> Faezeh
>>
>> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Thank you so much for you response. I should say that I know about what
>>> you are saying. My issue is that I have these 4 columns in my LUT file. Why
>>> and how can I change the numbers (RGB values) to create new LUT?
>>>
>>> Bests,
>>> Faezeh
>>>
>>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 Thank you so much for you descriptions. I checked out the link you just
 sent me. Because I do not have many experiences working with Freesurfer, I
 really could not understand about how I can do such this revising in LUT
 file. Can you explain more about this? I truly appreciate your time and
 help.

 Regards,
 Faezeh Vedaei

 On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei 
 wrote:
>
> Hi,
>
> I really appreciate you for help me in this process. May you clarify me
> from which pattern you changed the RGB values for that region? How I can
> change the coordinates for the others?
>
> Regards,
> Faezeh Vedaei
>
>
> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
> wrote:
>>
>> Hi,
>>
>> I should let you know that, it works! It shows paracentral name in
>> tksurfer. So, how I have to revise my .ctab file to get the right result?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> Thank you for your response. I just used the command you suggested to
>>> use by just a change in calling .ctab LUT file. I used the path:
>>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by 
>>> just
>>> calling aparc.annot.a2009s.ctab. It is strange that I created annot 
>>> file for
>>> lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
>>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
>>> opinion?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
>>> wrote:

 Hi,


 Here is the text format of those files.

 Regards,
 Faezeh Vedaei

 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

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

2016-03-02 Thread Faeze Vedaei

Hi,

Thank you for your response. sorry, I could not understand what you mean.
How you found 23 230 60 values for paracentral region? I mean. Are these
from Freesurfer LUT?

Regards,
Faezeh Vedaei

On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei  wrote:

> Thank you for your response. It is better to explain my question that the
> coordinates for paracentral in .ctab file is '63 100 60', that you changed
> these to '23 230 60' in your new version. My question is that how you
> applied such this change on the RBG values for this region?
>
> Regards,
> Faezeh
>
> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei 
> wrote:
>
>> Thank you so much for you response. I should say that I know about what
>> you are saying. My issue is that I have these 4 columns in my LUT file. Why
>> and how can I change the numbers (RGB values) to create new LUT?
>>
>> Bests,
>> Faezeh
>>
>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>> Thank you so much for you descriptions. I checked out the link you just
>>> sent me. Because I do not have many experiences working with Freesurfer, I
>>> really could not understand about how I can do such this revising in LUT
>>> file. Can you explain more about this? I truly appreciate your time and
>>> help.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei 
>>> wrote:
>>>
 Hi,

 I really appreciate you for help me in this process. May you clarify me
 from which pattern you changed the RGB values for that region? How I can
 change the coordinates for the others?

 Regards,
 Faezeh Vedaei


 On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
 wrote:

> Hi,
>
> I should let you know that, it works! It shows paracentral name in
> tksurfer. So, how I have to revise my .ctab file to get the right result?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> Thank you for your response. I just used the command you suggested to
>> use by just a change in calling .ctab LUT file. I used the path:
>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by 
>> just
>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file
>> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
>> opinion?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>>
>>> Here is the text format of those files.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> 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 <
 faezeved...@gmail.com> 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 <
> faezeved...@gmail.com> 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 <
>> faezeved...@gmail.com> 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

Re: [Freesurfer] hippocampus subfields

2016-03-02 Thread Eugenio Iglesias

OK now I get it ;-) 
You can simply do: 
mri_convert T2.FSspace.mgz T2.FSspace.resampled.mgz -odt float -rl 
[lr]h.hippoSfLabels-T1-T2.v10.mgz 
The rl flag says: "reslice like the following volume" 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Prabesh Kanel"  
To: "Freesurfer support list"  
Sent: Wednesday, March 2, 2016 8:31:17 PM 
Subject: Re: [Freesurfer] hippocampus subfields 




Hi Eugenio, 



Thank you, for your quick reply. It has happened to me in 4% of the cases, but 
my data sample is small like 100 data points. 



Addition to the second question: When I segment the hippocampus, I get the 
discrete segmentation volume at 0.333 mm resolution in the file 
[lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each 
voxel is labelled based on the subfield. I can use mri_extract_label or 
mri_binarize to extract individual subfield. But this segmentation will have 
voxels with the original label. If I load the file along with the 
T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the 
intensities at this place, I believe the intensity value is from 
T2.FSspace.mgz. Are those intensities values different from the original T2 
images? If not, Is it possible to get those value at each voxel location? 


Best Regards, 

Prabesh 


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 
 
Sent: Wednesday, March 2, 2016 12:23 PM 
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampus subfields 
Hi Prabesh, 
I think this is due to a bug that I found recently and which I'm trying to 
track down. Has it happened to you with many scans? The failure rate is less 
than 1% in my data. 
Regarding your second question: I'm sure it's not too trivial ;-) but I don't 
understand exactly what you mean. Do you want to deform the segmentations back 
to the original T2 space? 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Prabesh Kanel"  
To: "Freesurfer support list"  
Sent: Wednesday, March 2, 2016 6:07:13 PM 
Subject: [Freesurfer] hippocampus subfields 



Freesurfer List, 





I ran recon-all to segment hippocampus subfield using the development version 
of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and 
T2 images. But for some of the scans, the process stops at a point and doesn't 
seem to progress further. That happens in only a few cases and only when the 
data are run using the flag -hippocampal-subfields-T1T2. I have attached a log 
file of one of the case in this email. 

Another query that I have is to get T2 segmented subfields images (one with 
intensity values rather than labels). Is there an easier way to get T2 
subfields segmented images using the segmentation volumes and T2.FSspace.mgz. 
Sorry, if this question seems too trivial. 

Regards, 

Prabesh 

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Re: [Freesurfer] hippocampus subfields

2016-03-02 Thread Kanel, Prabesh


Hi Eugenio,


Thank you, for your quick reply. It has happened to me in 4% of the cases, but 
my data sample is small like 100 data points.


Addition to the second question: When I segment the hippocampus, I get the 
discrete segmentation volume at 0.333 mm resolution in the file 
[lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each 
voxel is labelled based on the subfield. I can use mri_extract_label or 
mri_binarize to extract individual subfield. But this segmentation will have 
voxels with the original label. If I load the file along with the 
T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the 
intensities at this place, I believe the intensity value is from 
T2.FSspace.mgz. Are those intensities values different from the original T2 
images? If not, Is it possible to get those value at each voxel location?


Best Regards,

Prabesh


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 

Sent: Wednesday, March 2, 2016 12:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampus subfields

Hi Prabesh,
I think this is due to a bug that I found recently and which I'm trying to 
track down. Has it happened to you with many scans? The failure rate is less 
than 1% in my data.
Regarding your second question: I'm sure it's not too trivial ;-)  but I don't 
understand exactly what you mean. Do you want to deform the segmentations back 
to the original T2 space?
Cheers,
Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


From: "Prabesh Kanel" 
To: "Freesurfer support list" 
Sent: Wednesday, March 2, 2016 6:07:13 PM
Subject: [Freesurfer] hippocampus subfields


Freesurfer List,


I ran recon-all to segment hippocampus subfield using the development version 
of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and 
T2 images. But for some of the scans, the process stops at a point and doesn't 
seem to progress further.  That happens in only a few cases and only when the 
data are run using the flag -hippocampal-subfields-T1T2. I have attached a log 
file of one of the case in this email.

Another query that I have is to get T2 segmented subfields images (one with 
intensity values rather than labels). Is there an easier way to get T2 
subfields segmented images using the segmentation volumes and T2.FSspace.mgz. 
Sorry, if this question seems too trivial.

Regards,

Prabesh

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Re: [Freesurfer] hippocampus subfields

2016-03-02 Thread Eugenio Iglesias

Hi Prabesh, 
I think this is due to a bug that I found recently and which I'm trying to 
track down. Has it happened to you with many scans? The failure rate is less 
than 1% in my data. 
Regarding your second question: I'm sure it's not too trivial ;-) but I don't 
understand exactly what you mean. Do you want to deform the segmentations back 
to the original T2 space? 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Prabesh Kanel"  
To: "Freesurfer support list"  
Sent: Wednesday, March 2, 2016 6:07:13 PM 
Subject: [Freesurfer] hippocampus subfields 



Freesurfer List, 





I ran recon-all to segment hippocampus subfield using the development version 
of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and 
T2 images. But for some of the scans, the process stops at a point and doesn't 
seem to progress further. That happens in only a few cases and only when the 
data are run using the flag -hippocampal-subfields-T1T2. I have attached a log 
file of one of the case in this email. 

Another query that I have is to get T2 segmented subfields images (one with 
intensity values rather than labels). Is there an easier way to get T2 
subfields segmented images using the segmentation volumes and T2.FSspace.mgz. 
Sorry, if this question seems too trivial. 

Regards, 

Prabesh 

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at 
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but does not contain patient information, please contact the sender and 
properly 
dispose of the e-mail. 
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[Freesurfer] Problem with mriconvert

2016-03-02 Thread Óscar Soto Angona

Hello,

We are medicine students who are using freesurfer for research. We had been
using freesurfer in Ubuntu 12.02 without encountering any trouble; recently
we updated to 14.04.

Now, when we attempt to convert a mgz file to nii using mriconvert, we have
an error regarding failure to write the files .nii

The command we are using is as follows:

mri_convert 
../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_seg.mgz
../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_
cortical_seg.nii


The error message we find is this one:

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/home/psa/datos_MRI_cerebral/estructural/Freesurfer_seg_cortical_resultado/C2090_cortical_seg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -4.74975e-08, 0)
j_ras = (0, 0, -1)
k_ras = (1.21072e-08, 1, 0)
writing to
../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii...
niiWrite(): error opening file
../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii
ERROR: failure writing
../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii


We really could use your help, since we can't find any solution in the
Internet. Thanks in advance for your attention.


Regards,


Óscar and Alba
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[Freesurfer] Deflate surface

2016-03-02 Thread marmaduke woodman

Hi

I would like to resample the cortical surface on the sphere at a lower 
resolution, and then deflate the surface to its folded form.

Is this something which can be done using the inflated surface that FS 
generates?

Thank you,
Marmaduke
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Re: [Freesurfer] Unknown option DKTatlas40

2016-03-02 Thread Watson, Christopher

The option should be:
--annot aparc.DKTatlas40

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of marmaduke woodman 
[marmaduke.wood...@univ-amu.fr]
Sent: Wednesday, March 2, 2016 08:27
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Unknown option DKTatlas40

hi

I'm using the dev version of FreeSurfer on 64-bit Fedora 23.

Recon-all runs fine but at the end I see

$ recon-all -s tvb -aparc2aseg
...
  mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --DKTatlas40

ERROR: Option --DKTatlas40 unknown

Running that command

$ mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos

without the --DKTatlas40 appears to run correctly.

Is this just an issue with the dev version or have I done something silly?

thanks,
Marmaduke

ps bugr output

FREESURFER_HOME: /opt/freesurfer

Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160229

RedHat release: Fedora release 23 (Twenty Three)

Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64

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

2016-03-02 Thread Bruce Fischl

No worries, it happens to all of us
Bruce

> On Mar 2, 2016, at 12:20 AM, Joseph Dien  wrote:
> 
> Oops, never mind.  User error.  I’m too embarrassed to even explain what I 
> did.  :)
> 
> Joe
> 
>> On Feb 29, 2016, at 21:38, Joseph Dien  wrote:
>> 
>> 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
>> InputRPA903  Main0.750.790.770.62
>> InputRPA906  Main0.810.810.830.74
>> InputRPA907  Main0.871   0.840.83
>> InputRPA908  Main0.910.930.950.89
>> InputRPA909  Main0.740.950.720.72
>> InputRPA910  Main0.850.960.810.79
>> InputRPA912  Main0.750.780.730.73
>> InputRPA914  Main0.7 0.850.830.81
>> InputRPA915  Main0.850.890.750.83
>> InputRPA916  Main0.840.920.870.72
>> InputRPA917  Main0.830.930.920.83
>> InputRPA918  Main0.870.910.790.85
>> InputRPA919  Main0.860.960.910.88
>> InputRPA920  Main0.840.920.870.84
>> InputRPA921  Main0.870.920.880.85
>> InputRPA922  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
>> 
>> 
>> 
>> 
>> 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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>> 
>> 
>> 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.
> 
> 
> 
> 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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[Freesurfer] conflicting Monte Carlo simulation results...

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

Re: [Freesurfer] Topological White Matter Correction

Re: [Freesurfer] hippocampus subfields

[Freesurfer] Topological White Matter Correction

Re: [Freesurfer] Unknown option DKTatlas40

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

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

Re: [Freesurfer] hippocampus subfields

Re: [Freesurfer] hippocampus subfields

Re: [Freesurfer] hippocampus subfields

[Freesurfer] Problem with mriconvert

[Freesurfer] Deflate surface

Re: [Freesurfer] Unknown option DKTatlas40

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

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