Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation

[Bruce Fischl]

eek, that's terrible! SO it's a standard FLASH scan? The TE is a bit 
long, but not terribly so. If you upload one of the subjects that did 
poorly I'll take a look. We try hard to be agnositc to many things, but if 
you know the sequence is fixed you can specifiy some of the contrast 
parameters once for the whole study and improve this a ton. I'm not sure 
I've ever seen one quite this bad though. What are the voxel dimensions?


cheers
Bruce


On Fri, 25 Mar 2016, Dr. Benson wrote:


Good.  Thanks.

On Fri, Mar 25, 2016 at 9:59 PM, Ramtilak Gattu 
wrote:

  Hello all,


   We have run recon -all on  some healthy control subjects T1
  images but we  found out that the gray-white segmentation on
  half our subjects is bad and it leads to increased white matter
  volumes and decreased gray matter volumes. I have included a
  snap shot showing the difference in segmentation from bad to
  good for 3 cases

https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts
/15/guestaccess.aspx?guestaccesstoken=ajPIRobFq548RyhRJWPQ9q70vAXUGIJ9h5WPD
  E1klUw%3d&docid=0dd4546a8004f46578b7a2177b192806a

  . The parameter in the  sequence are TE=4.92 ms, TR=19 ms, Flip
  angle =20 degrees. and use a snapshot one slice to show the good
  CNR.  We are using Freesurfer version 5.3.


  Thanks


  Regards

  Tilak.  


___
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.




--
 Medical Director--Center for Neurologic Studies
43000 W. 9 Mile Road
Novi, MI  48375
CNS Phone (248)277-3334
Cell: (248) 227-9814
Fax (586) 566-0178
Web: www.NeurologicStudies.com


***NOTICE*** The documents accompanying this email transmission contain
confidential information belonging to the sender, which is legally
privileged. The information is intended only for the use of the
individual(s) or entity(ies) named above. If you are not the intended
recipient, you are hereby notified that any disclosure, copying,
distribution, or the taking of any action in reliance on the contents of
this emailed information is strictly prohibited. If you have received this
email in error, please immediately notify us by telephone at 248-277-3334 to
arrange for return of the original documents to us. Thank you.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation

[Dr. Benson]

Good.  Thanks.

On Fri, Mar 25, 2016 at 9:59 PM, Ramtilak Gattu 
wrote:

> Hello all,
>
>
>  We have run recon -all on  some healthy control subjects T1 images but we
>  found out that the gray-white segmentation on half our subjects is bad and
> it leads to increased white matter volumes and decreased gray matter
> volumes. I have included a snap shot showing the difference in segmentation
> from bad to good for 3 cases
>
>
> https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/15/guestaccess.aspx?guestaccesstoken=ajPIRobFq548RyhRJWPQ9q70vAXUGIJ9h5WPDE1klUw%3d&docid=0dd4546a8004f46578b7a2177b192806a
>
> . The parameter in the  sequence are TE=4.92 ms, TR=19 ms, Flip angle =20
> degrees. and use a snapshot one slice to show the good CNR.  We are using
> Freesurfer version 5.3.
>
>
> Thanks
>
>
> Regards
>
> Tilak.
>
> ___
> 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.
>
>


-- 
 Medical Director--Center for Neurologic Studies
*43000 W. 9 Mile Road *
*Novi, MI  48375*
*CNS Phone (248)277-3334*
*Cell: (248) 227-9814*
*Fax (586) 566-0178*
Web: www.NeurologicStudies.com 

-- 
***NOTICE*** The documents accompanying this email transmission contain 
confidential information belonging to the sender, which is legally 
privileged. The information is intended only for the use of the 
individual(s) or entity(ies) named above. If you are not the intended 
recipient, you are hereby notified that any disclosure, copying, 
distribution, or the taking of any action in reliance on the contents of 
this emailed information is strictly prohibited. If you have received this 
email in error, please immediately notify us by telephone at 248-277-3334 
to arrange for return of the original documents to us. Thank you. 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] improving white/grey segmentation in recon -all for better volume estmation

[Ramtilak Gattu]

Hello all,


 We have run recon -all on  some healthy control subjects T1 images but we  
found out that the gray-white segmentation on half our subjects is bad and it 
leads to increased white matter volumes and decreased gray matter volumes. I 
have included a snap shot showing the difference in segmentation from bad to 
good for 3 cases

https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/15/guestaccess.aspx?guestaccesstoken=ajPIRobFq548RyhRJWPQ9q70vAXUGIJ9h5WPDE1klUw%3d&docid=0dd4546a8004f46578b7a2177b192806a

. The parameter in the  sequence are TE=4.92 ms, TR=19 ms, Flip angle =20 
degrees. and use a snapshot one slice to show the good CNR.  We are using 
Freesurfer version 5.3.


Thanks


Regards

Tilak.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] initial processing in devel 6.0 version and final stats processing in stable version 6.0?

[Lara Foland-Ross]

Hi Freesurfer experts, 

We'd like to begin a cortical thickness and hippocampal subfield analysis in 
the most recent devel version of FS. Can you please confirm that we will we be 
able to run the analysis of these data in the final stable release of 6.0?

Thanks,
Lara

Lara Foland-Ross, Ph.D.
Research Associate
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] whole hemisphere is yellow

[Miracle Ozzoude]

Hello Douglas, 
I just sent you the current file. Thank you. 
Best, 
Miracle 


From: Douglas N Greve 
Sent: March 25, 2016 9:35 PM
To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow

I meant the glmfit folder, which is

  lh.firstsessionscore1.glmdir


On 03/25/2016 02:29 PM, Miracle Ozzoude wrote:
> Hello Douglas,
> I have sent the files to you. Thank you.
> Best,
> Miracle
>
> 
> From: Douglas N Greve 
> Sent: March 25, 2016 6:11 PM
> To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
> not sure what is happening. Can you tar up the glmfit folder and send it to 
> me at our file drop?
>
>https://gate.nmr.mgh.harvard.edu/filedrop2
>
>
>
> On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
>> mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos  
>> --cwpvalthresh  0.05 --2spaces
>>
>> 
>> From: Douglas N Greve 
>> Sent: March 25, 2016 6:05 PM
>> To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>
>> what was your mri_glmfit-sim command line?
>>
>> On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
>>> Hello Bruce and Douglas,
>>> This is what my design looks like.
>>> GroupDescriptorFile 1
>>> Class Group1
>>> Class Group2
>>> Variables Age Firstsessionscore
>>> Input subj1 Group1 72 0.76
>>> Input subj2 Group1 67 0.43
>>> Input subj3 Group2 80 1.23
>>> The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to 
>>> investigate if thickness correlates with the score removing the effects of 
>>> group and age. The uncorrected map had blue and red colors in some areas of 
>>> the brain. The blue color (thickness decreases withe score) seems unlike 
>>> because i was expecting all red color(thickness increases with score). 
>>> After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, 
>>> I tried to view the corrected map however, my entire left hemisphere was 
>>> yellow with no clusters. how do i fix this?Thanks
>>> Miracle
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Douglas N Greve 
>>> 
>>> Sent: March 24, 2016 6:36 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>>
>>> Can you give us more info about the design and the contrast you are
>>> testing? What does the uncorrected map look like?
>>>
>>> On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
 I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the 
 precuneus area in yellow for one of my results however, for the other it 
 displayed the entire hemisphere in yellow. Do I need to use the 
 configure-- overlay? ‎Also, when I tried to view the cluster summary for 
 the entire hemisphere results, I did not see a single cluster unlike, the 
 cluster summary for the precuneus results

 Sent from my BlackBerry 10 smartphone.
   Original Message
 From: Bruce Fischl
 Sent: Thursday, March 24, 2016 9:48 AM
 To: Freesurfer support list
 Reply To: Freesurfer support list
 Subject: Re: [Freesurfer] whole hemisphere is yellow


 if it's all yellow it means everything is significant. What threshold are
 you using?
 On Thu, 24 Mar 2016, Miracle Ozzoude wrote:

> Hello Bruce,
> No. This was after I ran the correction for multiple comparisons. Do I 
> need to change the threshold too? My other results were fine. Thanks
> Best,
> Miracle
>
> Sent from my BlackBerry 10 smartphone.
>  Original Message
> From: Bruce Fischl
> Sent: Thursday, March 24, 2016 8:45 AM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
>
> Hi Miracle
>
> have you tried changing the thresholds? What kinds of values are you
> seeing?
>
> Bruce
> On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
>
>> hello doug,
>> i performed a group analysis and after correction for multiple 
>> comparisons when i tried to load the corrected clusters the whole 
>> hemisphere was completely yellow. what should i do?
>> Best,
>> Miracle
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it 
> is
> addressed. If you believe this e-mail was sent to you in error an

Re: [Freesurfer] whole hemisphere is yellow

[Douglas N Greve]

I meant the glmfit folder, which is

  lh.firstsessionscore1.glmdir


On 03/25/2016 02:29 PM, Miracle Ozzoude wrote:
> Hello Douglas,
> I have sent the files to you. Thank you.
> Best,
> Miracle
>
> 
> From: Douglas N Greve 
> Sent: March 25, 2016 6:11 PM
> To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
> not sure what is happening. Can you tar up the glmfit folder and send it to 
> me at our file drop?
>
>https://gate.nmr.mgh.harvard.edu/filedrop2
>
>
>
> On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
>> mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos  
>> --cwpvalthresh  0.05 --2spaces
>>
>> 
>> From: Douglas N Greve 
>> Sent: March 25, 2016 6:05 PM
>> To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>
>> what was your mri_glmfit-sim command line?
>>
>> On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
>>> Hello Bruce and Douglas,
>>> This is what my design looks like.
>>> GroupDescriptorFile 1
>>> Class Group1
>>> Class Group2
>>> Variables Age Firstsessionscore
>>> Input subj1 Group1 72 0.76
>>> Input subj2 Group1 67 0.43
>>> Input subj3 Group2 80 1.23
>>> The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to 
>>> investigate if thickness correlates with the score removing the effects of 
>>> group and age. The uncorrected map had blue and red colors in some areas of 
>>> the brain. The blue color (thickness decreases withe score) seems unlike 
>>> because i was expecting all red color(thickness increases with score). 
>>> After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, 
>>> I tried to view the corrected map however, my entire left hemisphere was 
>>> yellow with no clusters. how do i fix this?Thanks
>>> Miracle
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Douglas N Greve 
>>> 
>>> Sent: March 24, 2016 6:36 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>>
>>> Can you give us more info about the design and the contrast you are
>>> testing? What does the uncorrected map look like?
>>>
>>> On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
 I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the 
 precuneus area in yellow for one of my results however, for the other it 
 displayed the entire hemisphere in yellow. Do I need to use the 
 configure-- overlay? ‎Also, when I tried to view the cluster summary for 
 the entire hemisphere results, I did not see a single cluster unlike, the 
 cluster summary for the precuneus results

 Sent from my BlackBerry 10 smartphone.
   Original Message
 From: Bruce Fischl
 Sent: Thursday, March 24, 2016 9:48 AM
 To: Freesurfer support list
 Reply To: Freesurfer support list
 Subject: Re: [Freesurfer] whole hemisphere is yellow


 if it's all yellow it means everything is significant. What threshold are
 you using?
 On Thu, 24 Mar 2016, Miracle Ozzoude wrote:

> Hello Bruce,
> No. This was after I ran the correction for multiple comparisons. Do I 
> need to change the threshold too? My other results were fine. Thanks
> Best,
> Miracle
>
> Sent from my BlackBerry 10 smartphone.
>  Original Message
> From: Bruce Fischl
> Sent: Thursday, March 24, 2016 8:45 AM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
>
> Hi Miracle
>
> have you tried changing the thresholds? What kinds of values are you
> seeing?
>
> Bruce
> On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
>
>> hello doug,
>> i performed a group analysis and after correction for multiple 
>> comparisons when i tried to load the corrected clusters the whole 
>> hemisphere was completely yellow. what should i do?
>> Best,
>> Miracle
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it 
> is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the send

Re: [Freesurfer] Is it possible to use the mris_make_face_parcellation with the ico6 mesh?

[dgw]

first caveat, I could be wrong:

On Fri, Mar 25, 2016 at 3:18 PM, Michael Waskom  wrote:
> Hi,
>
> Can you say a bit more about what you mean?
>
>> If my memory serves, as you go to higher resolutions you end up with
>> multiple points being mapped to the same location,
>
> Do you mean multiple icosahedron vertices being mapped to the same native
> mesh vertex, or the other way around?

I can't remember correctly, this is one of those cases, where I remember it was
surprising and confusing, but can't remember what the right answer was
>
> In any case, the issue here is a little bit different, in that it is just
> raised when trying to generate a color table for the annotation:
> https://github.com/neurodebian/freesurfer/blob/master/utils/colortab.c#L540

I'm wondering if that is just a quirk of the error reporting, because
the check for
multiple vertices in FreeSurfer is at the colortab stage.

hth
d
>
> Michael
>
> On Fri, Mar 25, 2016 at 11:27 AM, dgw  wrote:
>>
>> Hi Michael,
>>
>> I think this is a problem that crops up periodically for us in the
>> MEEG world, where we use these downsampling
>> as calculated in MNE. If my memory serves, as you go to higher
>> resolutions you end up with multiple points
>> being mapped to the same location, which I don't believe we have ever
>> found a solution to. Note, this can even happen
>> at ico 5 (particularly on smaller brains).
>>
>>
>> hth
>> d
>>
>> On Fri, Mar 25, 2016 at 2:20 PM, Michael Waskom 
>> wrote:
>> > Hi Freesurfers,
>> >
>> > I'd like to use mris_make_face_parcellation to downsample an individual
>> > subject's surface mesh to a resolution similar to fsaverage6.
>> >
>> > My understanding is that mris_make_face_parcellation should let me do
>> > this,
>> > and it does what I expect with ic3-5. However when I run it with ic6 as
>> > the
>> > target, it fails:
>> >
>> > [surf]$ mris_make_face_parcellation lh.sphere
>> > $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot
>> > Reading lh.sphere
>> > Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri
>> > parcellating hemisphere into 40962 units
>> > INFO: CTABunique() could not find a unique set in 10 tries
>> > INFO: CTABunique() could not find a unique set in 100 tries
>> > ERROR: could not find a unique color table
>> >
>> > I don't really care if the colors themselves are distinct, and it should
>> > be
>> > possible to just programmatically generate a valid color table (since
>> > 255 ^
>> > 3 > 40962). I thought that providing a colortable with unique values
>> > through
>> > the -ctab option might work, but looking at the source code it seems
>> > that
>> > option will *write* a colortable, not read one.
>> >
>> > So, is there any way to accomplish the downsampling I want?
>> >
>> > Thanks in advance,
>> > Michael
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Is it possible to use the mris_make_face_parcellation with the ico6 mesh?

[Michael Waskom]

Hi,

Can you say a bit more about what you mean?

> If my memory serves, as you go to higher resolutions you end up with
multiple points being mapped to the same location,

Do you mean multiple icosahedron vertices being mapped to the same native
mesh vertex, or the other way around?

In any case, the issue here is a little bit different, in that it is just
raised when trying to generate a color table for the annotation:
https://github.com/neurodebian/freesurfer/blob/master/utils/colortab.c#L540

Michael

On Fri, Mar 25, 2016 at 11:27 AM, dgw  wrote:

> Hi Michael,
>
> I think this is a problem that crops up periodically for us in the
> MEEG world, where we use these downsampling
> as calculated in MNE. If my memory serves, as you go to higher
> resolutions you end up with multiple points
> being mapped to the same location, which I don't believe we have ever
> found a solution to. Note, this can even happen
> at ico 5 (particularly on smaller brains).
>
>
> hth
> d
>
> On Fri, Mar 25, 2016 at 2:20 PM, Michael Waskom 
> wrote:
> > Hi Freesurfers,
> >
> > I'd like to use mris_make_face_parcellation to downsample an individual
> > subject's surface mesh to a resolution similar to fsaverage6.
> >
> > My understanding is that mris_make_face_parcellation should let me do
> this,
> > and it does what I expect with ic3-5. However when I run it with ic6 as
> the
> > target, it fails:
> >
> > [surf]$ mris_make_face_parcellation lh.sphere
> > $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot
> > Reading lh.sphere
> > Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri
> > parcellating hemisphere into 40962 units
> > INFO: CTABunique() could not find a unique set in 10 tries
> > INFO: CTABunique() could not find a unique set in 100 tries
> > ERROR: could not find a unique color table
> >
> > I don't really care if the colors themselves are distinct, and it should
> be
> > possible to just programmatically generate a valid color table (since
> 255 ^
> > 3 > 40962). I thought that providing a colortable with unique values
> through
> > the -ctab option might work, but looking at the source code it seems that
> > option will *write* a colortable, not read one.
> >
> > So, is there any way to accomplish the downsampling I want?
> >
> > Thanks in advance,
> > Michael
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Gray-white segmentation

[Bruce Fischl]

Hi Randy

we need significantly more information from you if you want our help. 
What kind of scan are you talking about? Have you tried any intervention 
such as control points? Can you post an image or email us an example of one 
that fails?


cheers
Bruce


On Fri, 25 Mar 2016, Dr. Benson 
wrote:



I'm new to FreeSurfer.  Trying to do volumetric analysis on MPRAGE data but
on half of the studies the results are poor.  Specifically, the gray matter
volume is very small due to a poor segmentation of the white matter which
includes much of the cortical gray matter.  The contrast to noise is good
and not sure why I got a good result on some and not others.  Could use some
help on this, please.
Randy Benson, M.D.

--
 Medical Director--Center for Neurologic Studies
43000 W. 9 Mile Road
Novi, MI  48375
CNS Phone (248)277-3334
Cell: (248) 227-9814
Fax (586) 566-0178
Web: www.NeurologicStudies.com


***NOTICE*** The documents accompanying this email transmission contain
confidential information belonging to the sender, which is legally
privileged. The information is intended only for the use of the
individual(s) or entity(ies) named above. If you are not the intended
recipient, you are hereby notified that any disclosure, copying,
distribution, or the taking of any action in reliance on the contents of
this emailed information is strictly prohibited. If you have received this
email in error, please immediately notify us by telephone at 248-277-3334 to
arrange for return of the original documents to us. Thank you.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] whole hemisphere is yellow

[Miracle Ozzoude]

Hello Douglas, 
I have sent the files to you. Thank you. 
Best, 
Miracle 


From: Douglas N Greve 
Sent: March 25, 2016 6:11 PM
To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow

not sure what is happening. Can you tar up the glmfit folder and send it to me 
at our file drop?

  https://gate.nmr.mgh.harvard.edu/filedrop2



On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
> mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos  
> --cwpvalthresh  0.05 --2spaces
>
> 
> From: Douglas N Greve 
> Sent: March 25, 2016 6:05 PM
> To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
> what was your mri_glmfit-sim command line?
>
> On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
>> Hello Bruce and Douglas,
>> This is what my design looks like.
>> GroupDescriptorFile 1
>> Class Group1
>> Class Group2
>> Variables Age Firstsessionscore
>> Input subj1 Group1 72 0.76
>> Input subj2 Group1 67 0.43
>> Input subj3 Group2 80 1.23
>> The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to 
>> investigate if thickness correlates with the score removing the effects of 
>> group and age. The uncorrected map had blue and red colors in some areas of 
>> the brain. The blue color (thickness decreases withe score) seems unlike 
>> because i was expecting all red color(thickness increases with score). After 
>> I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I 
>> tried to view the corrected map however, my entire left hemisphere was 
>> yellow with no clusters. how do i fix this?Thanks
>> Miracle
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: March 24, 2016 6:36 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>
>> Can you give us more info about the design and the contrast you are
>> testing? What does the uncorrected map look like?
>>
>> On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
>>> I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the 
>>> precuneus area in yellow for one of my results however, for the other it 
>>> displayed the entire hemisphere in yellow. Do I need to use the configure-- 
>>> overlay? ‎Also, when I tried to view the cluster summary for the entire 
>>> hemisphere results, I did not see a single cluster unlike, the cluster 
>>> summary for the precuneus results
>>>
>>> Sent from my BlackBerry 10 smartphone.
>>>  Original Message
>>> From: Bruce Fischl
>>> Sent: Thursday, March 24, 2016 9:48 AM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>>
>>>
>>> if it's all yellow it means everything is significant. What threshold are
>>> you using?
>>> On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
>>>
 Hello Bruce,
 No. This was after I ran the correction for multiple comparisons. Do I 
 need to change the threshold too? My other results were fine. Thanks
 Best,
 Miracle

 Sent from my BlackBerry 10 smartphone.
 Original Message
 From: Bruce Fischl
 Sent: Thursday, March 24, 2016 8:45 AM
 To: Freesurfer support list
 Reply To: Freesurfer support list
 Subject: Re: [Freesurfer] whole hemisphere is yellow


 Hi Miracle

 have you tried changing the thresholds? What kinds of values are you
 seeing?

 Bruce
 On Wed, 23 Mar 2016, Miracle Ozzoude wrote:

> hello doug,
> i performed a group analysis and after correction for multiple 
> comparisons when i tried to load the corrected clusters the whole 
> hemisphere was completely yellow. what should i do?
> Best,
> Miracle
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 The information in this e-mail is intended only for the person to whom it 
 is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



>>

Re: [Freesurfer] Is it possible to use the mris_make_face_parcellation with the ico6 mesh?

[dgw]

Hi Michael,

I think this is a problem that crops up periodically for us in the
MEEG world, where we use these downsampling
as calculated in MNE. If my memory serves, as you go to higher
resolutions you end up with multiple points
being mapped to the same location, which I don't believe we have ever
found a solution to. Note, this can even happen
at ico 5 (particularly on smaller brains).


hth
d

On Fri, Mar 25, 2016 at 2:20 PM, Michael Waskom  wrote:
> Hi Freesurfers,
>
> I'd like to use mris_make_face_parcellation to downsample an individual
> subject's surface mesh to a resolution similar to fsaverage6.
>
> My understanding is that mris_make_face_parcellation should let me do this,
> and it does what I expect with ic3-5. However when I run it with ic6 as the
> target, it fails:
>
> [surf]$ mris_make_face_parcellation lh.sphere
> $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot
> Reading lh.sphere
> Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri
> parcellating hemisphere into 40962 units
> INFO: CTABunique() could not find a unique set in 10 tries
> INFO: CTABunique() could not find a unique set in 100 tries
> ERROR: could not find a unique color table
>
> I don't really care if the colors themselves are distinct, and it should be
> possible to just programmatically generate a valid color table (since 255 ^
> 3 > 40962). I thought that providing a colortable with unique values through
> the -ctab option might work, but looking at the source code it seems that
> option will *write* a colortable, not read one.
>
> So, is there any way to accomplish the downsampling I want?
>
> Thanks in advance,
> Michael
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Is it possible to use the mris_make_face_parcellation with the ico6 mesh?

[Michael Waskom]

Hi Freesurfers,

I'd like to use mris_make_face_parcellation to downsample an individual
subject's surface mesh to a resolution similar to fsaverage6.

My understanding is that mris_make_face_parcellation should let me do this,
and it does what I expect with ic3-5. However when I run it with ic6 as the
target, it fails:

[surf]$ mris_make_face_parcellation lh.sphere
$FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot
Reading lh.sphere
Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri
parcellating hemisphere into 40962 units
INFO: CTABunique() could not find a unique set in 10 tries
INFO: CTABunique() could not find a unique set in 100 tries
ERROR: could not find a unique color table

I don't really care if the colors themselves are distinct, and it should be
possible to just programmatically generate a valid color table (since 255 ^
3 > 40962). I thought that providing a colortable with unique values
through the -ctab option might work, but looking at the source code it
seems that option will *write* a colortable, not read one.

So, is there any way to accomplish the downsampling I want?

Thanks in advance,
Michael
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] whole hemisphere is yellow

[Miracle Ozzoude]

also, i do require a username and password in order to send you the folder. 


From: Douglas N Greve 
Sent: March 25, 2016 6:11 PM
To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow

not sure what is happening. Can you tar up the glmfit folder and send it to me 
at our file drop?

  https://gate.nmr.mgh.harvard.edu/filedrop2



On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
> mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos  
> --cwpvalthresh  0.05 --2spaces
>
> 
> From: Douglas N Greve 
> Sent: March 25, 2016 6:05 PM
> To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
> what was your mri_glmfit-sim command line?
>
> On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
>> Hello Bruce and Douglas,
>> This is what my design looks like.
>> GroupDescriptorFile 1
>> Class Group1
>> Class Group2
>> Variables Age Firstsessionscore
>> Input subj1 Group1 72 0.76
>> Input subj2 Group1 67 0.43
>> Input subj3 Group2 80 1.23
>> The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to 
>> investigate if thickness correlates with the score removing the effects of 
>> group and age. The uncorrected map had blue and red colors in some areas of 
>> the brain. The blue color (thickness decreases withe score) seems unlike 
>> because i was expecting all red color(thickness increases with score). After 
>> I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I 
>> tried to view the corrected map however, my entire left hemisphere was 
>> yellow with no clusters. how do i fix this?Thanks
>> Miracle
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: March 24, 2016 6:36 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>
>> Can you give us more info about the design and the contrast you are
>> testing? What does the uncorrected map look like?
>>
>> On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
>>> I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the 
>>> precuneus area in yellow for one of my results however, for the other it 
>>> displayed the entire hemisphere in yellow. Do I need to use the configure-- 
>>> overlay? ‎Also, when I tried to view the cluster summary for the entire 
>>> hemisphere results, I did not see a single cluster unlike, the cluster 
>>> summary for the precuneus results
>>>
>>> Sent from my BlackBerry 10 smartphone.
>>>  Original Message
>>> From: Bruce Fischl
>>> Sent: Thursday, March 24, 2016 9:48 AM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>>
>>>
>>> if it's all yellow it means everything is significant. What threshold are
>>> you using?
>>> On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
>>>
 Hello Bruce,
 No. This was after I ran the correction for multiple comparisons. Do I 
 need to change the threshold too? My other results were fine. Thanks
 Best,
 Miracle

 Sent from my BlackBerry 10 smartphone.
 Original Message
 From: Bruce Fischl
 Sent: Thursday, March 24, 2016 8:45 AM
 To: Freesurfer support list
 Reply To: Freesurfer support list
 Subject: Re: [Freesurfer] whole hemisphere is yellow


 Hi Miracle

 have you tried changing the thresholds? What kinds of values are you
 seeing?

 Bruce
 On Wed, 23 Mar 2016, Miracle Ozzoude wrote:

> hello doug,
> i performed a group analysis and after correction for multiple 
> comparisons when i tried to load the corrected clusters the whole 
> hemisphere was completely yellow. what should i do?
> Best,
> Miracle
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 The information in this e-mail is intended only for the person to whom it 
 is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] whole hemisphere is yellow

[Miracle Ozzoude]

this is the contrast file with the corrected and uncorrected map right? 
miracle 


From: Douglas N Greve 
Sent: March 25, 2016 6:11 PM
To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow

not sure what is happening. Can you tar up the glmfit folder and send it to me 
at our file drop?

  https://gate.nmr.mgh.harvard.edu/filedrop2



On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
> mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos  
> --cwpvalthresh  0.05 --2spaces
>
> 
> From: Douglas N Greve 
> Sent: March 25, 2016 6:05 PM
> To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
> what was your mri_glmfit-sim command line?
>
> On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
>> Hello Bruce and Douglas,
>> This is what my design looks like.
>> GroupDescriptorFile 1
>> Class Group1
>> Class Group2
>> Variables Age Firstsessionscore
>> Input subj1 Group1 72 0.76
>> Input subj2 Group1 67 0.43
>> Input subj3 Group2 80 1.23
>> The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to 
>> investigate if thickness correlates with the score removing the effects of 
>> group and age. The uncorrected map had blue and red colors in some areas of 
>> the brain. The blue color (thickness decreases withe score) seems unlike 
>> because i was expecting all red color(thickness increases with score). After 
>> I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I 
>> tried to view the corrected map however, my entire left hemisphere was 
>> yellow with no clusters. how do i fix this?Thanks
>> Miracle
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: March 24, 2016 6:36 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>
>> Can you give us more info about the design and the contrast you are
>> testing? What does the uncorrected map look like?
>>
>> On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
>>> I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the 
>>> precuneus area in yellow for one of my results however, for the other it 
>>> displayed the entire hemisphere in yellow. Do I need to use the configure-- 
>>> overlay? ‎Also, when I tried to view the cluster summary for the entire 
>>> hemisphere results, I did not see a single cluster unlike, the cluster 
>>> summary for the precuneus results
>>>
>>> Sent from my BlackBerry 10 smartphone.
>>>  Original Message
>>> From: Bruce Fischl
>>> Sent: Thursday, March 24, 2016 9:48 AM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>>
>>>
>>> if it's all yellow it means everything is significant. What threshold are
>>> you using?
>>> On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
>>>
 Hello Bruce,
 No. This was after I ran the correction for multiple comparisons. Do I 
 need to change the threshold too? My other results were fine. Thanks
 Best,
 Miracle

 Sent from my BlackBerry 10 smartphone.
 Original Message
 From: Bruce Fischl
 Sent: Thursday, March 24, 2016 8:45 AM
 To: Freesurfer support list
 Reply To: Freesurfer support list
 Subject: Re: [Freesurfer] whole hemisphere is yellow


 Hi Miracle

 have you tried changing the thresholds? What kinds of values are you
 seeing?

 Bruce
 On Wed, 23 Mar 2016, Miracle Ozzoude wrote:

> hello doug,
> i performed a group analysis and after correction for multiple 
> comparisons when i tried to load the corrected clusters the whole 
> hemisphere was completely yellow. what should i do?
> Best,
> Miracle
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 The information in this e-mail is intended only for the person to whom it 
 is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

[Douglas N Greve]

On 03/24/2016 07:37 PM, Joseph Dien wrote:
> Doug, I see now what your concern was with just adjusting the beta 
> weights.  Since FSFAST is using a pseudo-mixed effects model, there is 
> also a need to pass the cesvar statistics up to the second level.  How 
> that might accommodate the derivative boost computation is not 
> straightforward to me.  I need to understand better what fsfast is 
> doing.  I was wondering if you could answer a couple questions about 
> how cesvar is computed;
>
> 1) The cesvar computations in the fast_fratio.m function provided a 
> good guide.  According to it:
> cescvm = inv(C*inv(X'*X)*X'*Sn*X*inv(X'*X)*C’);
> where Sn is the covariance matrix of the noise after the whitening 
> (which is on by default).
> cesvar=rvar./cescvm.
>
> How is Sn computed?
The autocorrelation function is computed at each voxel from the 
residual, these are fit to an AR1 model and adjusted for residual bias. 
They are spatially clustered based on AR1 value. The Sn is computed as a 
toeplitz matrix of the autocorrelation function derived from the 
best-fit AR1 model (that matrix is multipled by the residual variance to 
get the final Sn).
>
> 2) I need to understand what fsfast is doing conceptually but I 
> couldn’t reconcile the Thirion et al (2007) Equation #5 and the 
> equations above, specifically the inclusion of the rvar term.  Can you 
> throw some light on this?
It is really nothing fancy, just down-weighting each subject by the 
residual standard deviation.
>
> I greatly appreciate your helpful tips and this amazing software that 
> you have written.
>
> Respectfully,
>
> Joe
>
>
>> On Mar 17, 2016, at 15:48, Joseph Dien > > wrote:
>>
>> I did more digging around and came up with a procedure.  Please let 
>> me know if it would cause any problems.
>> Looking at the contents of the X.mat files (which contain the 
>> predictors), it appears that the betas are indeed arranged as c1 d1 
>> c2 d2…
>> I also found that isxconcat-sess requires the contrast output 
>> of mkcontrast-sess so I can’t just bypass it.
>>
>> So my thought is:
>>
>> 1) run mkanalysis-sess with -spmhrf 1
>> 2) run selxavg3-sess with the -no-con-ok flag to get the spmhrf1 
>> betas without bothering with the contrasts
>> 3) run mkanalysis-sess with -spmhrf 0
>> 4) run selxavg3-sess again but with the contrasts to get everything 
>> set up
>> 5) read in the spmhrf1 betas with MRIread and compute the Calhoun 
>> derivative boost with the beta values in mri.vol
>> 6) use these values to compute the desired contrasts.  From my 
>> examination of a sample ces.nii.gz file, a simple linear combination 
>> based on the contrast weights is all that is needed.
>> 7) replace the contents of the corresponding spmhrf0 ces.nii.gz 
>> files’ mri.vol with these new values
>> 8) write out the new ces.nii.gz files.
>> 9) proceed with the analysis stream, using isxconcat-sess to set up 
>> the second level analysis
>>
>> So the question is, would this work?  Am I neglecting files other 
>> than ces.nii.gz that would need to be modified?  or other fields in 
>> the mri data structure?
>> When you referred to writing “out a new volume” is this what you meant?
>>
>> Thanks again for this help!
>>
>> Joe
>>
>>
>>> On Mar 15, 2016, at 17:32, Joseph Dien >> > wrote:
>>>
>>> oh duh!  Sorry, wasn’t thinking clearly.
>>> Okay, I see how to generate the betas now.  I don’t even need to 
>>> mess with the mkcontrast-sess command.
>>> I just run selxavg3-sess with the -no-con-ok flag.
>>> With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each 
>>> vertex.
>>> With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each 
>>> vertex.
>>> With 12 conditions, 12 more betas is exactly right.
>>> So how do I know which of the betas is which?
>>> I looked through the files and couldn’t find any labels.
>>> I’m guessing the first twelve are the condition betas for "spmhrf 0".
>>> If so, for "spmhrf 1", is it arranged as:
>>>
>>> 1) c1 c2 c3…d1 d2 d3...
>>>
>>> or
>>>
>>> 2) c1 d1 c2 d2...
>>>
>>>  (where d is the first derivative term)
>>>
>>> also, when I asked you earlier about implementing this procedure, I 
>>> had suggested reading the betas, computing the Calhoun, then 
>>> generating new beta.nii.gz files with the new betas replacing the 
>>> original spmhrf0 betas and then continuing with the regular analysis 
>>> stream but you said it would result in invalid p-values.  Instead, 
>>> you suggested:
>>>
>>> "I was just thinking you could load the beta into matlab, make the
>>> Calhoun computations on each condition, then compute the contrasts, then
>>> write out the new volume”
>>>
>>> can you expand on how one might “compute the contrasts” and “write 
>>> out the new volume”?
>>>
>>> Thanks again for this help!
>>>
>>> Joe
>>>
>>>
 On Mar 15, 2016, at 12:43, Douglas N Greve 
 mailto:gr...@nmr.mgh.harvard.edu>> wrote:

 The setwdelay is an option for mkcontrast-sess (

Re: [Freesurfer] whole hemisphere is yellow

[Douglas N Greve]

not sure what is happening. Can you tar up the glmfit folder and send it to me 
at our file drop?

  https://gate.nmr.mgh.harvard.edu/filedrop2



On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
> mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos  
> --cwpvalthresh  0.05 --2spaces
>
> 
> From: Douglas N Greve 
> Sent: March 25, 2016 6:05 PM
> To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
> what was your mri_glmfit-sim command line?
>
> On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
>> Hello Bruce and Douglas,
>> This is what my design looks like.
>> GroupDescriptorFile 1
>> Class Group1
>> Class Group2
>> Variables Age Firstsessionscore
>> Input subj1 Group1 72 0.76
>> Input subj2 Group1 67 0.43
>> Input subj3 Group2 80 1.23
>> The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to 
>> investigate if thickness correlates with the score removing the effects of 
>> group and age. The uncorrected map had blue and red colors in some areas of 
>> the brain. The blue color (thickness decreases withe score) seems unlike 
>> because i was expecting all red color(thickness increases with score). After 
>> I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I 
>> tried to view the corrected map however, my entire left hemisphere was 
>> yellow with no clusters. how do i fix this?Thanks
>> Miracle
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: March 24, 2016 6:36 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>
>> Can you give us more info about the design and the contrast you are
>> testing? What does the uncorrected map look like?
>>
>> On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
>>> I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the 
>>> precuneus area in yellow for one of my results however, for the other it 
>>> displayed the entire hemisphere in yellow. Do I need to use the configure-- 
>>> overlay? ‎Also, when I tried to view the cluster summary for the entire 
>>> hemisphere results, I did not see a single cluster unlike, the cluster 
>>> summary for the precuneus results
>>>
>>> Sent from my BlackBerry 10 smartphone.
>>>  Original Message
>>> From: Bruce Fischl
>>> Sent: Thursday, March 24, 2016 9:48 AM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>>
>>>
>>> if it's all yellow it means everything is significant. What threshold are
>>> you using?
>>> On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
>>>
 Hello Bruce,
 No. This was after I ran the correction for multiple comparisons. Do I 
 need to change the threshold too? My other results were fine. Thanks
 Best,
 Miracle

 Sent from my BlackBerry 10 smartphone.
 Original Message
 From: Bruce Fischl
 Sent: Thursday, March 24, 2016 8:45 AM
 To: Freesurfer support list
 Reply To: Freesurfer support list
 Subject: Re: [Freesurfer] whole hemisphere is yellow


 Hi Miracle

 have you tried changing the thresholds? What kinds of values are you
 seeing?

 Bruce
 On Wed, 23 Mar 2016, Miracle Ozzoude wrote:

> hello doug,
> i performed a group analysis and after correction for multiple 
> comparisons when i tried to load the corrected clusters the whole 
> hemisphere was completely yellow. what should i do?
> Best,
> Miracle
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 The information in this e-mail is intended only for the person to whom it 
 is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurf

Re: [Freesurfer] whole hemisphere is yellow

[Miracle Ozzoude]

mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos  
--cwpvalthresh  0.05 --2spaces


From: Douglas N Greve 
Sent: March 25, 2016 6:05 PM
To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow

what was your mri_glmfit-sim command line?

On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
> Hello Bruce and Douglas,
> This is what my design looks like.
> GroupDescriptorFile 1
> Class Group1
> Class Group2
> Variables Age Firstsessionscore
> Input subj1 Group1 72 0.76
> Input subj2 Group1 67 0.43
> Input subj3 Group2 80 1.23
> The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate 
> if thickness correlates with the score removing the effects of group and age. 
> The uncorrected map had blue and red colors in some areas of the brain. The 
> blue color (thickness decreases withe score) seems unlike because i was 
> expecting all red color(thickness increases with score). After I correcting 
> for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the 
> corrected map however, my entire left hemisphere was yellow with no clusters. 
> how do i fix this?Thanks
> Miracle
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: March 24, 2016 6:36 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
> Can you give us more info about the design and the contrast you are
> testing? What does the uncorrected map look like?
>
> On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
>> I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the 
>> precuneus area in yellow for one of my results however, for the other it 
>> displayed the entire hemisphere in yellow. Do I need to use the configure-- 
>> overlay? ‎Also, when I tried to view the cluster summary for the entire 
>> hemisphere results, I did not see a single cluster unlike, the cluster 
>> summary for the precuneus results
>>
>> Sent from my BlackBerry 10 smartphone.
>> Original Message
>> From: Bruce Fischl
>> Sent: Thursday, March 24, 2016 9:48 AM
>> To: Freesurfer support list
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>
>>
>> if it's all yellow it means everything is significant. What threshold are
>> you using?
>> On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
>>
>>> Hello Bruce,
>>> No. This was after I ran the correction for multiple comparisons. Do I need 
>>> to change the threshold too? My other results were fine. Thanks
>>> Best,
>>> Miracle
>>>
>>> Sent from my BlackBerry 10 smartphone.
>>>Original Message
>>> From: Bruce Fischl
>>> Sent: Thursday, March 24, 2016 8:45 AM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>>
>>>
>>> Hi Miracle
>>>
>>> have you tried changing the thresholds? What kinds of values are you
>>> seeing?
>>>
>>> Bruce
>>> On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
>>>
 hello doug,
 i performed a group analysis and after correction for multiple comparisons 
 when i tried to load the corrected clusters the whole hemisphere was 
 completely yellow. what should i do?
 Best,
 Miracle
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> 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.mg

Re: [Freesurfer] whole hemisphere is yellow

[Douglas N Greve]

what was your mri_glmfit-sim command line?

On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
> Hello Bruce and Douglas,
> This is what my design looks like.
> GroupDescriptorFile 1
> Class Group1
> Class Group2
> Variables Age Firstsessionscore
> Input subj1 Group1 72 0.76
> Input subj2 Group1 67 0.43
> Input subj3 Group2 80 1.23
> The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate 
> if thickness correlates with the score removing the effects of group and age. 
> The uncorrected map had blue and red colors in some areas of the brain. The 
> blue color (thickness decreases withe score) seems unlike because i was 
> expecting all red color(thickness increases with score). After I correcting 
> for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the 
> corrected map however, my entire left hemisphere was yellow with no clusters. 
> how do i fix this?Thanks
> Miracle
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: March 24, 2016 6:36 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
> Can you give us more info about the design and the contrast you are
> testing? What does the uncorrected map look like?
>
> On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
>> I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the 
>> precuneus area in yellow for one of my results however, for the other it 
>> displayed the entire hemisphere in yellow. Do I need to use the configure-- 
>> overlay? ‎Also, when I tried to view the cluster summary for the entire 
>> hemisphere results, I did not see a single cluster unlike, the cluster 
>> summary for the precuneus results
>>
>> Sent from my BlackBerry 10 smartphone.
>> Original Message
>> From: Bruce Fischl
>> Sent: Thursday, March 24, 2016 9:48 AM
>> To: Freesurfer support list
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>
>>
>> if it's all yellow it means everything is significant. What threshold are
>> you using?
>> On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
>>
>>> Hello Bruce,
>>> No. This was after I ran the correction for multiple comparisons. Do I need 
>>> to change the threshold too? My other results were fine. Thanks
>>> Best,
>>> Miracle
>>>
>>> Sent from my BlackBerry 10 smartphone.
>>>Original Message
>>> From: Bruce Fischl
>>> Sent: Thursday, March 24, 2016 8:45 AM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>>
>>>
>>> Hi Miracle
>>>
>>> have you tried changing the thresholds? What kinds of values are you
>>> seeing?
>>>
>>> Bruce
>>> On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
>>>
 hello doug,
 i performed a group analysis and after correction for multiple comparisons 
 when i tried to load the corrected clusters the whole hemisphere was 
 completely yellow. what should i do?
 Best,
 Miracle
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 

Re: [Freesurfer] whole hemisphere is yellow

[Miracle Ozzoude]

Hello Bruce and Douglas, 
This is what my design looks like. 
GroupDescriptorFile 1
Class Group1
Class Group2
Variables Age Firstsessionscore
Input subj1 Group1 72 0.76
Input subj2 Group1 67 0.43
Input subj3 Group2 80 1.23
The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate 
if thickness correlates with the score removing the effects of group and age. 
The uncorrected map had blue and red colors in some areas of the brain. The 
blue color (thickness decreases withe score) seems unlike because i was 
expecting all red color(thickness increases with score). After I correcting for 
multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the 
corrected map however, my entire left hemisphere was yellow with no clusters. 
how do i fix this?Thanks
Miracle 

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

Sent: March 24, 2016 6:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow

Can you give us more info about the design and the contrast you are
testing? What does the uncorrected map look like?

On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
> I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus 
> area in yellow for one of my results however, for the other it displayed the 
> entire hemisphere in yellow. Do I need to use the configure-- overlay? ‎Also, 
> when I tried to view the cluster summary for the entire hemisphere results, I 
> did not see a single cluster unlike, the cluster summary for the precuneus 
> results
>
> Sent from my BlackBerry 10 smartphone.
>Original Message
> From: Bruce Fischl
> Sent: Thursday, March 24, 2016 9:48 AM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
>
> if it's all yellow it means everything is significant. What threshold are
> you using?
> On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
>
>> Hello Bruce,
>> No. This was after I ran the correction for multiple comparisons. Do I need 
>> to change the threshold too? My other results were fine. Thanks
>> Best,
>> Miracle
>>
>> Sent from my BlackBerry 10 smartphone.
>>   Original Message
>> From: Bruce Fischl
>> Sent: Thursday, March 24, 2016 8:45 AM
>> To: Freesurfer support list
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>
>>
>> Hi Miracle
>>
>> have you tried changing the thresholds? What kinds of values are you
>> seeing?
>>
>> Bruce
>> On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
>>
>>> hello doug,
>>> i performed a group analysis and after correction for multiple comparisons 
>>> when i tried to load the corrected clusters the whole hemisphere was 
>>> completely yellow. what should i do?
>>> Best,
>>> Miracle
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Gray-white segmentation

[Dr. Benson]

I'm new to FreeSurfer.  Trying to do volumetric analysis on MPRAGE data but
on half of the studies the results are poor.  Specifically, the gray matter
volume is very small due to a poor segmentation of the white matter which
includes much of the cortical gray matter.  The contrast to noise is good
and not sure why I got a good result on some and not others.  Could use
some help on this, please.

Randy Benson, M.D.

-- 
 Medical Director--Center for Neurologic Studies
*43000 W. 9 Mile Road *
*Novi, MI  48375*
*CNS Phone (248)277-3334*
*Cell: (248) 227-9814*
*Fax (586) 566-0178*
Web: www.NeurologicStudies.com 

-- 
***NOTICE*** The documents accompanying this email transmission contain 
confidential information belonging to the sender, which is legally 
privileged. The information is intended only for the use of the 
individual(s) or entity(ies) named above. If you are not the intended 
recipient, you are hereby notified that any disclosure, copying, 
distribution, or the taking of any action in reliance on the contents of 
this emailed information is strictly prohibited. If you have received this 
email in error, please immediately notify us by telephone at 248-277-3334 
to arrange for return of the original documents to us. Thank you. 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Cortical thickness average

[Douglas N Greve]

mri_concat subject1/lh.thickness.fsaverage.mgh subect2/lh ... --mean --o 
lh.thickness.fsaverage.mean.mgh


On 03/24/2016 07:24 PM, Sahil Bajaj wrote:
> Hello FreeSurfer community,
>
> I calculated cortical thickness for 100 controls following the 
> instructions described here: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>
> So I have 100 lh.thickness.fsaverage.mgh, one for each subject. I was 
> wondering if there is any way to average the thickness over these 100 
> lh.thickness.fsaverage.mgh files to get one final 
> lh.thickness.fsaverage.mgh
>
> I am interested in calculating cortical thickness for 15 previously 
> defined ROIs, but I do not want to calculate 15x100 text files using 
> mri_segstats i.e. 15 text files for each subject and then average over 
> those but I would rather prefer to average over 100 
> lh.thickness.fsaverage.mgh files first and then calculate thickness 
> for each ROI to get 11 text files.
>
> Any help would be really appreciated.
>
> Thanks,
> Sahil
> -- 
> -
> Sahil Bajaj
> Post-doctoral Fellow
> Nantz National Alzheimer's Center, Department of Neurology
> The Houston Methodist Research Institute (THMRI)
> Houston, TX, USA.
> E-mail:sahil.br...@gmail.com 
>
>
> ___
> 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.

Re: [Freesurfer] Regarding: oblique view

[Bruce Fischl]

Hi Sampada

the problem isn't the oblique orientation it is the resolution (too low!) 
and contrast (not enough!). Can you give us the details of the scan? 
Resolution, type, etc?


cheers
Bruce
On Fri, 25 Mar 2016, Dr Sampada Sinha wrote:


Hello Bruce,

Please find enclosed snapshots of actual volume and wm_aseg.mgz (horizontal and
coronal view). Also in case, if I need to send the image over will you please 
let me
know where do I send it? Appreciate all your help.

Thanks and regards,

Sampada

On Thu, Mar 24, 2016 at 6:20 PM, Bruce Fischl  
wrote:
  HI Sampada

  wow, something went terribly wrong. Can you post an image of the actual
  volume and maybe of the wm segmentation?

  cheers
  Bruce

  On Thu, 24 Mar 2016, Dr Sampada Sinha wrote:

Hello Bruce,

The recon-all -autorecon2 process exited with the error. The
lh inflated no fix image
is attached with this email. I am also, attaching the
mri_info and recon_all.log with
this email. I am basically trying to calculate the lGI of 
the participants. I was
having issues with lGI but, its sorted noe. Will appreciate
if I can be guided by you
about how to fix this. I found the same kind of surface in
another participants.

With thanks and regards,

Sampada

On Tue, Mar 22, 2016 at 10:41 PM, Dr Sampada Sinha
 wrote:
      Hello Bruce,
Thanks again for your prompt response. We have an official
holiday here. Will
send the info on Thursday.

Thanks and regards,
Sampada
Predoctoral student
KGMU, Lko
India 

On haveay, March 2016, Bruce Fischl
 wrote:
      I see

      if you have defects that large you should look at the
      inflated.nofix surface to see what they are.

      What is your voxel resolution?

      cheers
      Bruce

      On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:

            Thanks Bruce for your reply. I did run it thru'
            recon-all. It went for more than 2
            days and then exited with XL defect error (convex
hull
            was more than 14000 and vertex
            size about 54000). So today I started by running
the
            recon-all in parts. I did not
            find anything wrong with brainmask files after
running
            autorecon1. I am presently
            running the autorecon-2 process. Will get back
with the
            surf files when this process
            is over.
            Thank you again for your reply and support.

            Kind regards, 

            Sampada

            On Tuesday, March 22, 2016, Bruce Fischl
             wrote:
                  sure. Have you tried running it through
            recon-all? It may work fine
                  On
                  Tue, 22 Mar 2016, Dr Sampada Sinha wrote:

                  > Thanks Bruce for your reply. The
acquisition
            was oblique and the voxel
                  size doesn't
                  > conform to the 1mm cube isotropic. I am
trying
            to work on it and figure
                  out a
                  > solution. However, if I am not, hope its
okay
            to send you the nifti
                  image.
                  > Thanks and regards,
                  >
                  > Sampada
                  >
                  >
                  >
                  > Rnday, March 20, 2016, Bruce Fischl
             wrote:
                  >       what do you mean by "adding" an
oblique
            angle? If you mean
                  acquiring the
                  >       data obliquely you should be fine
as long
            as the voxels are close
                  to 1mm
                  >       isotropic.
                  >
                  >       cheers
                  >       Bruce
                  >       On Sun, 20 Mar 2016, Dr Sampada
Sinha
            wrote:
                  >
                  >       > Dear freesurfer experts,

Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Kirstie Whitaker]

I think eroding the region makes sense in general - you just have to be careful 
to exclude subjects who end up with no data (as you discovered!)

You could also look into why these three subjects had such small wm regions 
under entorhinal cortex. My (still) suspicious mind wonders if there is a bad 
reconstruction that is cutting out part of the inferior temporal lobe and 
therefore "squeezing" all of the cortical labels into a smaller volume. This 
would in turn give very small wm volumes.

On the other hand, entorhinal cortex may just have a relatively small amount of 
white matter underlying it because it's so "narrow" such that when you erode by 
1mm you are left with nothing for these three subjects.

Glad you figured out the odd correlations!

Kx

Sent from my iPhone, please excuse any typos or excessive brevity

> On 25 Mar 2016, at 01:22, Elijah Mak  wrote:
> 
> Hi Kirstie,
> 
> Yes indeed there were 3 subjects at the bottom-left of the plot. 
> 
> To account for PV, I eroded the boundaries using -seg-erode 1 during the 
> mri_segstats stage, and this resulted in a few subjects with no data for the 
> WM entorhinal region (although these were saved as "0" in the .stats file). 
> Do people generally do this for DTI studies?
> 
> All good now. 
> 
> Many thanks again, Kirstie.
> 
> Best Wishes,
> Elijah
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.