Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces

[Bruce Fischl]

the vox2ras. Not sure about the HCP pipeline. They use a deprecated 
version of FS, but in any case what you had would not work as the ?h.pial 
surface didn't match the ?h.white.deformed one. If you also deformed 
the pial it would be ok

  On Wed, 23 Nov 2016, Antonin 
Skoch wrote:

> Dear Bruce,
> 
> thank you very much for your time.
> 
> Concerning transformations, that is weird since I adopted my code from HCP 
> pipelines
> 
> https://github.com/Washington-University/Pipelines/blob/master/FreeSurfer/scripts/FreeSu
> rferHiresPial.sh
> 
> and there I think they use the surfaces precisely this way. They are using 
> the surfaces
> generated by 1mm3 volumes as input and refine them by using co-registered 
> higher
> resolution volumes. I use full-hires reconstruction, but for my safety and 
> convenience I
> left the code with transformations, which (I thought) should do not any harm 
> (there is
> not any resampling in my case).
> 
> I also checked the white and white.deformed processed by default HCP pipeline 
> and they do
> NOT have the same ras2vox.
> 
> BTW, which transformation in mris_info is relevant for this case? I found 
> several of them
> in mris_info:
> 
> talairch.xfm
> 
> surfaceRAS to talaraiched surfaceRAS
> 
> talairached surfaceRAS to surfaceRAS
> 
> Volume Geometry vox2ras
> 
> Volume Geometry vox2ras-tkr
> 
> Antonin
> 
> 
> From: Bruce Fischl 
> To: Antonin Skoch 
> Sent: 11/23/2016 12:42 AM
> Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement 
> -issue with
> overlapping pial surfaces
>
>   yes, and I tracked it down and fixed it. BTW: don't use the
>   white.deformed surface - use the white one. You can't use one surface 
> that
>   has been transformed (i.e. has a different ras2vox) and other surfaces 
> that
>   have not (you can see this if you run mris_info on the surface files, 
> the
>   ras2vox should match in all of them)
>
>   cheers
>   Bruce
> 
> 
> 
>
___
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] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces

[Antonin Skoch]

Dear Bruce,

thank you very much for your time. 

Concerning transformations, that is weird since I adopted my code from HCP 
pipelines 

https://github.com/Washington-University/Pipelines/blob/master/FreeSurfer/scripts/FreeSurferHiresPial.sh

and there I think they use the surfaces precisely this way. They are using the 
surfaces generated by 1mm3 volumes as input and refine them by using 
co-registered higher resolution volumes. I use full-hires reconstruction, but 
for my safety and convenience I left the code with transformations, which (I 
thought) should do not any harm (there is not any resampling in my case).

I also checked the white and white.deformed processed by default HCP pipeline 
and they do NOT have the same ras2vox.

BTW, which transformation in mris_info is relevant for this case? I found 
several of them in mris_info:

talairch.xfm

surfaceRAS to talaraiched surfaceRAS

talairached surfaceRAS to surfaceRAS

Volume Geometry vox2ras

Volume Geometry vox2ras-tkr

Antonin



 From:   Bruce Fischl  
 To:   Antonin Skoch  
 Sent:   11/23/2016 12:42 AM 
 Subject:   Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement 
-issue with overlapping pial surfaces 

yes, and I tracked it down and fixed it. BTW: don't use the  
white.deformed surface - use the white one. You can't use one surface that  
has been transformed (i.e. has a different ras2vox) and other surfaces that  
have not (you can see this if you run mris_info on the surface files, the  
ras2vox should match in all of them) 
 
cheers 
Bruce 
 

___
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] mris_make_surfaces in longitudinal stream - explanation of parameters

[Bruce Fischl]

Hi Antonin

in the case of severe atrophy or a long period between scans the pial 
surface from time 1 may be far enough outside the pial surface of time 2 
that the deformation cannot recover it. We have found that starting it a 
bit inside makes it more robust.


As for the mris_longitudinal_surfaces there are lots of binaries that we 
develop and try out that aren't used in recon-all but might be some day


cheers
Bruce


On Tue, 22 Nov 2016, Antonin Skoch wrote:


Dear Martin,

thank you for the explanations, and sorry, I missed your previous response.

Just I am wondering, what is the reason of the shrinkage? Why not to start 
directly from
pial surface of the base?

And, I also found a binary mris_longitudinal_surfaces, which is, however, not 
used in
recon-all. What is the significance of this binary?

Antonin

---

Hi Antonin, 


max does not constrain thickness. The location of the max is constrained to be 
within 2*m
ax for every iteration, so it will constrain how far outwards it searches. But 
it will be
 done at each scale, so it can still deform a long way.

We initialize the surface processing in long with the surface from the base. 
But we don’t
 use the pial from base directly, instead we shrink it a little first and start 
from ther
e.

Not sure about the last question (difference between orig and prig-white parameters). 


Best, Martin


> On Nov 14, 2016, at 10:17 PM, Antonin Skoch  wrote:
> 
> Dear experts,
> 
> I am trying to understand how the pial and white surfaces are generated in longitudinal

 stream using information from the reconstructed base template (freeSurfer 
development ve
rsion). 
> 
> In longitudinal stream, apart from the -orig, -orig_pial and -orig_white there are also

 parameters -long and -max 3.5.
> 
> May I ask what is the significance of these parameters?
> 
>  -max 3.5 means constraining cortical thickness to 3.5 mm? Why this constraint is appli

ed specifically in longitudinal stream?
> 
> In mris_make_surfaces.c I found that -long means that initial pial vertex positions are

 set between final white and orig pial, slightly inside orig_pial. What is the 
significan
ce of this setting in longitudinal stream?
> 
> Last question, not related specifically to longitudinal stream: What is the difference 
between -orig and -orig_white parameters of mris_make_surfaces? From the reading of sourc

e codes (quite tough to me) I got an impression that from -orig the gray and 
white matter
 histogram values are computed whereas -orig_white defines initial position of 
the vertic
es in the first iteration (which, for some reasons, does not necessary has to 
be identica
l to -orig). Am I correct?
> 
> Regards,
> 
> Antonin Skoch

> ___
> Freesurfer mailing list
> Freesurfer at 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] mris_make_surfaces in longitudinal stream - explanation of parameters

[Antonin Skoch]

Dear Martin,

thank you for the explanations, and sorry, I missed your previous response.

Just I am wondering, what is the reason of the shrinkage? Why not to start 
directly from pial surface of the base?

And, I also found a binary mris_longitudinal_surfaces, which is, however, not 
used in recon-all. What is the significance of this binary?

Antonin

---

Hi Antonin, 

max does not constrain thickness. The location of the max is constrained to be 
within 2*max for every iteration, so it will constrain how far outwards it 
searches. But it will be done at each scale, so it can still deform a long way.

We initialize the surface processing in long with the surface from the base. 
But we don’t use the pial from base directly, instead we shrink it a little 
first and start from there.

Not sure about the last question (difference between orig and prig-white 
parameters). 

Best, Martin


> On Nov 14, 2016, at 10:17 PM, Antonin Skoch  wrote:
> 
> Dear experts,
> 
> I am trying to understand how the pial and white surfaces are generated in 
> longitudinal stream using information from the reconstructed base template 
> (freeSurfer development version). 
> 
> In longitudinal stream, apart from the -orig, -orig_pial and -orig_white 
> there are also parameters -long and -max 3.5.
> 
> May I ask what is the significance of these parameters?
> 
>  -max 3.5 means constraining cortical thickness to 3.5 mm? Why this 
> constraint is applied specifically in longitudinal stream?
> 
> In mris_make_surfaces.c I found that -long means that initial pial vertex 
> positions are set between final white and orig pial, slightly inside 
> orig_pial. What is the significance of this setting in longitudinal stream?
> 
> Last question, not related specifically to longitudinal stream: What is the 
> difference between -orig and -orig_white parameters of mris_make_surfaces? 
> From the reading of source codes (quite tough to me) I got an impression that 
> from -orig the gray and white matter histogram values are computed whereas 
> -orig_white defines initial position of the vertices in the first iteration 
> (which, for some reasons, does not necessary has to be identical to -orig). 
> Am I correct?
> 
> Regards,
> 
> Antonin Skoch
> ___
> Freesurfer mailing list
> Freesurfer at 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] Longitudinal stream : LME and limits of model

[Matthieu Vanhoutte]

Hi Martin,

Please see inline below:

> Le 22 nov. 2016 à 17:04, Martin Reuter  a écrit :
> 
> Hi Matthieu, 
> (also inline)
> 
>> On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte 
>> > wrote:
>> 
>> Hi Martin,
>> 
>> Thanks for replying. Please see inline below:
>> 
>>> Le 21 nov. 2016 à 20:26, Martin Reuter >> > a écrit :
>>> 
>>> Hi Matthieu, 
>>> 
>>> a few quick answers. Maybe Jorge knows more. 
>>> Generally number of subjects / time points etc. cannot be specified 
>>> generally. All depends on how noisy your data is and how large the effect 
>>> is that you expect to detect. You can do a power analysis in order to 
>>> figure out how many subject / time points would be needed. There are some 
>>> tools for that in the LME toolbox:
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#Poweranalysis
>>>  
>>> 
>>>  
>>> 
>>> 1. see above
>>> 2. yes, also time points can miss from the middle. If you have mainly 
>>> missing time points at the end, this will bias your analysis to some 
>>> extend, as the remaining ones may be extremely healthy, as probably the 
>>> more diseased ones drop out. You may want to do a time-to-event (or 
>>> survival-analysis) which considers early drop-out.
>> 
>> Is there any way to do with Freesurfer this kind of analysis ?
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/SurvivalAnalysis 
>  
> Yes, there is also a paper where we do this. It is a combination of LME and 
> Survival Analysis (as for the SA you need to have measurements of all 
> subjects at all time points, so you estimate that from the LME model). 

Thank you for the link, I will take a look at. So if understand, this analysis 
has to be done after LME statistical analysis ? Thereafter since SA need all 
time points, LME model will allow me to estimate missing time points ?

> 
>> 
>>> 3. see above (power analysis)
>>> 4. GIGO means garbage in, garbage out, so the less you QC, the more likely 
>>> will your results be junk. The more you QC the less likely will it be junk, 
>>> but could still be. The FS wiki has lots of tutorial information on 
>>> checking freesurfer recons. For longitudinal, you should additionally check 
>>> the surfaces in the base, the brain mask in the base, and the alignment of 
>>> the time points (although there is some wiggle space for the alignment, as 
>>> most things are allowed to evolve further for each time point). 
>> 
>> For the alignment of the time points, should I better comparing brainmask or 
>> norm.mgz ?
> 
> It does not really matter, I would use norm.mgz. I would load images on top 
> of each other and then use the opacity slider in Freeview to blend between 
> them (that way the eye can pick up small motions). I would not worry too much 
> about local deformations which could be caused by non-linearity (gradient). 
> But if you see global misalignment (rotation, translation) it is a cause for 
> concern) .

Ok thank you. The non-linearity you are talking about are well provoked by MRI 
system and not non-linear registration between time points and template base, 
aren’t they ?

Best regards,
Matthieu

> 
>> 
>> In order to avoid bias by adding further time points in the model by the 
>> -add recon all command, is this better for each subject to take into account 
>> all the time points existing for it or only the ones that I will include in 
>> the model (three time points / subject ; if existing 6 time points for any 
>> subject ?)
>> 
> 
> Usually it is recommended to run all time points in the model (so a base with 
> 6 time points) and not use the - - add flag. Also, Linear Mixed Effects 
> models deal well with missing time points. It is perfectly OK to have 
> differently many time points per subject for that. You should still check if 
> there is a bias (e.g. one group always has 3 time points the other 6) that 
> would not be good. Maybe also consult with a local biostatistician if you are 
> not comfortable with the stats. The LME tools are matlab, and so are the 
> survival-analysis scripts. 
> 
> Best, Martin
> 
> 
> 
>> Best regards,
>> Matthieu
>> 
>>> 
>>> Best, Martin
>>> 
 On Nov 21, 2016, at 7:07 PM, Matthieu Vanhoutte 
 > wrote:
 
 Dear Freesurfer’s experts,
 
 I would have some questions regarding the LME model to be used in 
 longitudinal stream:
 
 1) Which are the ratio limits or % of missing timepoints accepted ? 
 (according time, I have less and less subjects time points)
 
 2) Is it possible to include patients that would miss the first timepoint 
 but got the others ?
 
 3) Considering a group in 

Re: [Freesurfer] quantifyHippocampalSubfields.sh

[Alan Francis]

Wonderful. Thank you so much.

best,

Alan

On Tue, Nov 22, 2016 at 1:42 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Hi again,
> The command should be:
> quantifyHippocampalSubfields.sh T1 Cannabis_HSF.txt
>
>
>
> Juan Eugenio Iglesias
> ERC Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 22 Nov 2016, at 18:00, Alan Francis  wrote:
>
> Hi Eugenio -
>
> The command I used was :
>
> [afrancis-mac:/Applications/freesurfer/subjects] afrancis%
> quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt
>
> Here are a listing of the files in the mri directory of a given brain:
>
> [afrancis-mac:subjects/DM_130/mri] afrancis% ls -la
> total 89392
> drwxr-xr-x  47 afrancis  wheel  1598 Nov 16 14:03 .
> drwxr-xr-x  13 afrancis  wheel   442 Nov  2 01:48 ..
> -rw-rw-r--   1 afrancis  wheel   4938244 Nov 16 02:13 T1.mgz
> -rw-rw-r--   1 afrancis  wheel396646 Nov 16 12:24 aparc+aseg.mgz
> -rw-rw-r--   1 afrancis  wheel428024 Nov 16 12:26 aparc.a2009s+aseg.mgz
> -rw-rw-r--   1 afrancis  wheel226733 Nov 16 05:49 aseg.auto.mgz
> -rw-rw-r--   1 afrancis  wheel  1545 Nov 16 05:18
> aseg.auto_noCCseg.label_intensities.txt
> -rw-rw-r--   1 afrancis  wheel226279 Nov 16 05:48 aseg.auto_noCCseg.mgz
> -rw-rw-r--   1 afrancis  wheel338726 Nov 16 12:26 aseg.mgz
> -rw-rw-r--   1 afrancis  wheel226785 Nov 16 12:21
> aseg.presurf.hypos.mgz
> -rw-rw-r--   1 afrancis  wheel226733 Nov 16 05:49 aseg.presurf.mgz
> -rw-rw-r--   1 afrancis  wheel   1266179 Nov 16 05:53 brain.finalsurfs.mgz
> -rw-rw-r--   1 afrancis  wheel   1266179 Nov 16 05:53 brain.mgz
> -rw-rw-r--   1 afrancis  wheel   1245588 Nov 16 02:14 brainmask.auto.mgz
> -rw-rw-r--   1 afrancis  wheel   1245588 Nov 16 02:14 brainmask.mgz
> -rw-rw-r--   1 afrancis  wheel480682 Nov 16 02:46 ctrl_pts.mgz
> -rw-rw-r--   1 afrancis  wheel130178 Nov 16 05:57 filled.mgz
> -rw-rw-r--   1 afrancis  wheel 68968 Nov 16 13:31
> lh.hippoSfLabels-T1.v10.T1space.mgz
> -rw-rw-r--   1 afrancis  wheel 56338 Nov 16 13:31
> lh.hippoSfLabels-T1.v10.mgz
> -rw-rw-r--   1 afrancis  wheel   286 Nov 16 13:30
> lh.hippoSfVolumes-T1.v10.txt
> -rw-rw-r--   1 afrancis  wheel109443 Nov 16 12:09 lh.ribbon.mgz
> -rw-rw-r--   1 afrancis  wheel 17518 Nov 16 02:27
> mri_nu_correct.mni.log
> -rw-rw-r--   1 afrancis  wheel 14530 Nov 16 02:10
> mri_nu_correct.mni.log.bak
> -rw-rw-r--   1 afrancis  wheel   1348717 Nov 16 02:46 norm.mgz
> -rw-rw-r--   1 afrancis  wheel   3934641 Nov 16 02:27 nu.mgz
> -rw-rw-r--   1 afrancis  wheel   2897650 Nov 16 04:50 nu_noneck.mgz
> drwxr-xr-x   3 afrancis  wheel   102 Oct 25 11:23 orig
> -rw-rw-r--   1 afrancis  wheel   5959814 Nov 16 02:00 orig.mgz
> -rw-rw-r--   1 afrancis  wheel   6015638 Nov 16 02:10 orig_nu.mgz
> -rw-r--r--   1 afrancis  wheel  10522408 Nov 16 02:00 rawavg.mgz
> -rw-rw-r--   1 afrancis  wheel 68830 Nov 16 14:03
> rh.hippoSfLabels-T1.v10.T1space.mgz
> -rw-rw-r--   1 afrancis  wheel 56219 Nov 16 14:03
> rh.hippoSfLabels-T1.v10.mgz
> -rw-rw-r--   1 afrancis  wheel   286 Nov 16 14:03
> rh.hippoSfVolumes-T1.v10.txt
> -rw-rw-r--   1 afrancis  wheel110421 Nov 16 12:09 rh.ribbon.mgz
> -rw-rw-r--   1 afrancis  wheel207344 Nov 16 12:09 ribbon.mgz
> -rw-rw-r--   1 afrancis  wheel   119 Nov 16 05:54 segment.dat
> -rw-rw-r--   1 afrancis  wheel  1546 Nov 16 03:43
> talairach.label_intensities.txt
> -rw-rw-r--   1 afrancis  wheel   428 Nov 16 02:44 talairach.log
> -rw-rw-r--   1 afrancis  wheel   214 Nov  2 02:25
> talairach_with_skull.log
> -rw-rw-r--   1 afrancis  wheel   428 Nov 16 05:03
> talairach_with_skull_2.log
> drwxrwxr-x  14 afrancis  wheel   476 Nov 16 02:10 transforms
> -rw-rw-r--   1 afrancis  wheel377180 Nov 16 05:56 wm.asegedit.mgz
> -rw-rw-r--   1 afrancis  wheel377870 Nov 16 05:56 wm.mgz
> -rw-rw-r--   1 afrancis  wheel422925 Nov 16 05:56 wm.seg.mgz
> -rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm1.txt
> -rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm255.txt
> -rw-rw-r--   1 afrancis  wheel447425 Nov 16 12:36 wmparc.mgz
>
> thanks so much,
>
> Alan
>
> On Tue, Nov 22, 2016 at 12:33 PM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
>> Hi Alan,
>> Can you please send the the command line that you used to generate the
>> results, and a listing of the files in the mri directory of any subject
>> you’ve analyzed?
>> Cheers,
>> /Eugenio
>>
>> Juan Eugenio Iglesias
>> ERC Senior Research Fellow
>> Translational Imaging Group
>> University College London
>> http://www.jeiglesias.com
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> On 22 Nov 2016, at 16:48, Alan Francis  wrote:
>>
>> Hi Eugenio -
>>
>> Hope all is well with you at UCL. I have the run the subfields algorithm
>> on a set of subjects using Freesurfer 6.0. All the brains were 

Re: [Freesurfer] quantifyHippocampalSubfields.sh

[Iglesias Gonzalez, Eugenio]

Hi again,
The command should be:
quantifyHippocampalSubfields.sh T1 Cannabis_HSF.txt



Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 22 Nov 2016, at 18:00, Alan Francis 
> wrote:

Hi Eugenio -

The command I used was :

[afrancis-mac:/Applications/freesurfer/subjects] afrancis% 
quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt

Here are a listing of the files in the mri directory of a given brain:

[afrancis-mac:subjects/DM_130/mri] afrancis% ls -la
total 89392
drwxr-xr-x  47 afrancis  wheel  1598 Nov 16 14:03 .
drwxr-xr-x  13 afrancis  wheel   442 Nov  2 01:48 ..
-rw-rw-r--   1 afrancis  wheel   4938244 Nov 16 02:13 T1.mgz
-rw-rw-r--   1 afrancis  wheel396646 Nov 16 12:24 aparc+aseg.mgz
-rw-rw-r--   1 afrancis  wheel428024 Nov 16 12:26 aparc.a2009s+aseg.mgz
-rw-rw-r--   1 afrancis  wheel226733 Nov 16 05:49 aseg.auto.mgz
-rw-rw-r--   1 afrancis  wheel  1545 Nov 16 05:18 
aseg.auto_noCCseg.label_intensities.txt
-rw-rw-r--   1 afrancis  wheel226279 Nov 16 05:48 aseg.auto_noCCseg.mgz
-rw-rw-r--   1 afrancis  wheel338726 Nov 16 12:26 aseg.mgz
-rw-rw-r--   1 afrancis  wheel226785 Nov 16 12:21 aseg.presurf.hypos.mgz
-rw-rw-r--   1 afrancis  wheel226733 Nov 16 05:49 aseg.presurf.mgz
-rw-rw-r--   1 afrancis  wheel   1266179 Nov 16 05:53 brain.finalsurfs.mgz
-rw-rw-r--   1 afrancis  wheel   1266179 Nov 16 05:53 brain.mgz
-rw-rw-r--   1 afrancis  wheel   1245588 Nov 16 02:14 brainmask.auto.mgz
-rw-rw-r--   1 afrancis  wheel   1245588 Nov 16 02:14 brainmask.mgz
-rw-rw-r--   1 afrancis  wheel480682 Nov 16 02:46 ctrl_pts.mgz
-rw-rw-r--   1 afrancis  wheel130178 Nov 16 05:57 filled.mgz
-rw-rw-r--   1 afrancis  wheel 68968 Nov 16 13:31 
lh.hippoSfLabels-T1.v10.T1space.mgz
-rw-rw-r--   1 afrancis  wheel 56338 Nov 16 13:31 
lh.hippoSfLabels-T1.v10.mgz
-rw-rw-r--   1 afrancis  wheel   286 Nov 16 13:30 
lh.hippoSfVolumes-T1.v10.txt
-rw-rw-r--   1 afrancis  wheel109443 Nov 16 12:09 lh.ribbon.mgz
-rw-rw-r--   1 afrancis  wheel 17518 Nov 16 02:27 mri_nu_correct.mni.log
-rw-rw-r--   1 afrancis  wheel 14530 Nov 16 02:10 mri_nu_correct.mni.log.bak
-rw-rw-r--   1 afrancis  wheel   1348717 Nov 16 02:46 norm.mgz
-rw-rw-r--   1 afrancis  wheel   3934641 Nov 16 02:27 nu.mgz
-rw-rw-r--   1 afrancis  wheel   2897650 Nov 16 04:50 nu_noneck.mgz
drwxr-xr-x   3 afrancis  wheel   102 Oct 25 11:23 orig
-rw-rw-r--   1 afrancis  wheel   5959814 Nov 16 02:00 orig.mgz
-rw-rw-r--   1 afrancis  wheel   6015638 Nov 16 02:10 orig_nu.mgz
-rw-r--r--   1 afrancis  wheel  10522408 Nov 16 02:00 rawavg.mgz
-rw-rw-r--   1 afrancis  wheel 68830 Nov 16 14:03 
rh.hippoSfLabels-T1.v10.T1space.mgz
-rw-rw-r--   1 afrancis  wheel 56219 Nov 16 14:03 
rh.hippoSfLabels-T1.v10.mgz
-rw-rw-r--   1 afrancis  wheel   286 Nov 16 14:03 
rh.hippoSfVolumes-T1.v10.txt
-rw-rw-r--   1 afrancis  wheel110421 Nov 16 12:09 rh.ribbon.mgz
-rw-rw-r--   1 afrancis  wheel207344 Nov 16 12:09 ribbon.mgz
-rw-rw-r--   1 afrancis  wheel   119 Nov 16 05:54 segment.dat
-rw-rw-r--   1 afrancis  wheel  1546 Nov 16 03:43 
talairach.label_intensities.txt
-rw-rw-r--   1 afrancis  wheel   428 Nov 16 02:44 talairach.log
-rw-rw-r--   1 afrancis  wheel   214 Nov  2 02:25 talairach_with_skull.log
-rw-rw-r--   1 afrancis  wheel   428 Nov 16 05:03 talairach_with_skull_2.log
drwxrwxr-x  14 afrancis  wheel   476 Nov 16 02:10 transforms
-rw-rw-r--   1 afrancis  wheel377180 Nov 16 05:56 wm.asegedit.mgz
-rw-rw-r--   1 afrancis  wheel377870 Nov 16 05:56 wm.mgz
-rw-rw-r--   1 afrancis  wheel422925 Nov 16 05:56 wm.seg.mgz
-rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm1.txt
-rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm255.txt
-rw-rw-r--   1 afrancis  wheel447425 Nov 16 12:36 wmparc.mgz

thanks so much,

Alan

On Tue, Nov 22, 2016 at 12:33 PM, Iglesias Gonzalez, Eugenio 
> wrote:
Hi Alan,
Can you please send the the command line that you used to generate the results, 
and a listing of the files in the mri directory of any subject you’ve analyzed?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 22 Nov 2016, at 16:48, Alan Francis 
> wrote:

Hi Eugenio -

Hope all is well with you at UCL. I have the run the subfields algorithm on a 
set of subjects using Freesurfer 6.0. All the brains were processed without 
much fuss. However, when I ran the following:

quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt

It yielded nothing.

Can you please help me?

Thanks,

Alan

--

Re: [Freesurfer] quantifyHippocampalSubfields.sh

[Alan Francis]

Hi Eugenio -

The command I used was :

[afrancis-mac:/Applications/freesurfer/subjects] afrancis%
quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt

Here are a listing of the files in the mri directory of a given brain:

[afrancis-mac:subjects/DM_130/mri] afrancis% ls -la
total 89392
drwxr-xr-x  47 afrancis  wheel  1598 Nov 16 14:03 .
drwxr-xr-x  13 afrancis  wheel   442 Nov  2 01:48 ..
-rw-rw-r--   1 afrancis  wheel   4938244 Nov 16 02:13 T1.mgz
-rw-rw-r--   1 afrancis  wheel396646 Nov 16 12:24 aparc+aseg.mgz
-rw-rw-r--   1 afrancis  wheel428024 Nov 16 12:26 aparc.a2009s+aseg.mgz
-rw-rw-r--   1 afrancis  wheel226733 Nov 16 05:49 aseg.auto.mgz
-rw-rw-r--   1 afrancis  wheel  1545 Nov 16 05:18
aseg.auto_noCCseg.label_intensities.txt
-rw-rw-r--   1 afrancis  wheel226279 Nov 16 05:48 aseg.auto_noCCseg.mgz
-rw-rw-r--   1 afrancis  wheel338726 Nov 16 12:26 aseg.mgz
-rw-rw-r--   1 afrancis  wheel226785 Nov 16 12:21 aseg.presurf.hypos.mgz
-rw-rw-r--   1 afrancis  wheel226733 Nov 16 05:49 aseg.presurf.mgz
-rw-rw-r--   1 afrancis  wheel   1266179 Nov 16 05:53 brain.finalsurfs.mgz
-rw-rw-r--   1 afrancis  wheel   1266179 Nov 16 05:53 brain.mgz
-rw-rw-r--   1 afrancis  wheel   1245588 Nov 16 02:14 brainmask.auto.mgz
-rw-rw-r--   1 afrancis  wheel   1245588 Nov 16 02:14 brainmask.mgz
-rw-rw-r--   1 afrancis  wheel480682 Nov 16 02:46 ctrl_pts.mgz
-rw-rw-r--   1 afrancis  wheel130178 Nov 16 05:57 filled.mgz
-rw-rw-r--   1 afrancis  wheel 68968 Nov 16 13:31
lh.hippoSfLabels-T1.v10.T1space.mgz
-rw-rw-r--   1 afrancis  wheel 56338 Nov 16 13:31
lh.hippoSfLabels-T1.v10.mgz
-rw-rw-r--   1 afrancis  wheel   286 Nov 16 13:30
lh.hippoSfVolumes-T1.v10.txt
-rw-rw-r--   1 afrancis  wheel109443 Nov 16 12:09 lh.ribbon.mgz
-rw-rw-r--   1 afrancis  wheel 17518 Nov 16 02:27 mri_nu_correct.mni.log
-rw-rw-r--   1 afrancis  wheel 14530 Nov 16 02:10
mri_nu_correct.mni.log.bak
-rw-rw-r--   1 afrancis  wheel   1348717 Nov 16 02:46 norm.mgz
-rw-rw-r--   1 afrancis  wheel   3934641 Nov 16 02:27 nu.mgz
-rw-rw-r--   1 afrancis  wheel   2897650 Nov 16 04:50 nu_noneck.mgz
drwxr-xr-x   3 afrancis  wheel   102 Oct 25 11:23 orig
-rw-rw-r--   1 afrancis  wheel   5959814 Nov 16 02:00 orig.mgz
-rw-rw-r--   1 afrancis  wheel   6015638 Nov 16 02:10 orig_nu.mgz
-rw-r--r--   1 afrancis  wheel  10522408 Nov 16 02:00 rawavg.mgz
-rw-rw-r--   1 afrancis  wheel 68830 Nov 16 14:03
rh.hippoSfLabels-T1.v10.T1space.mgz
-rw-rw-r--   1 afrancis  wheel 56219 Nov 16 14:03
rh.hippoSfLabels-T1.v10.mgz
-rw-rw-r--   1 afrancis  wheel   286 Nov 16 14:03
rh.hippoSfVolumes-T1.v10.txt
-rw-rw-r--   1 afrancis  wheel110421 Nov 16 12:09 rh.ribbon.mgz
-rw-rw-r--   1 afrancis  wheel207344 Nov 16 12:09 ribbon.mgz
-rw-rw-r--   1 afrancis  wheel   119 Nov 16 05:54 segment.dat
-rw-rw-r--   1 afrancis  wheel  1546 Nov 16 03:43
talairach.label_intensities.txt
-rw-rw-r--   1 afrancis  wheel   428 Nov 16 02:44 talairach.log
-rw-rw-r--   1 afrancis  wheel   214 Nov  2 02:25
talairach_with_skull.log
-rw-rw-r--   1 afrancis  wheel   428 Nov 16 05:03
talairach_with_skull_2.log
drwxrwxr-x  14 afrancis  wheel   476 Nov 16 02:10 transforms
-rw-rw-r--   1 afrancis  wheel377180 Nov 16 05:56 wm.asegedit.mgz
-rw-rw-r--   1 afrancis  wheel377870 Nov 16 05:56 wm.mgz
-rw-rw-r--   1 afrancis  wheel422925 Nov 16 05:56 wm.seg.mgz
-rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm1.txt
-rw-rw-r--   1 afrancis  wheel29 Nov 16 05:54 wm255.txt
-rw-rw-r--   1 afrancis  wheel447425 Nov 16 12:36 wmparc.mgz

thanks so much,

Alan

On Tue, Nov 22, 2016 at 12:33 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Hi Alan,
> Can you please send the the command line that you used to generate the
> results, and a listing of the files in the mri directory of any subject
> you’ve analyzed?
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> ERC Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 22 Nov 2016, at 16:48, Alan Francis  wrote:
>
> Hi Eugenio -
>
> Hope all is well with you at UCL. I have the run the subfields algorithm
> on a set of subjects using Freesurfer 6.0. All the brains were processed
> without much fuss. However, when I ran the following:
>
> quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt
>
> It yielded nothing.
>
> Can you please help me?
>
> Thanks,
>
> Alan
>
> --
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
> * Alan N. Francis PhD*
> Instructor - Imaging Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu 
> afran...@mclean.harvard.edu
>
>
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
> ___
> Freesurfer 

Re: [Freesurfer] quantifyHippocampalSubfields.sh

[Iglesias Gonzalez, Eugenio]

Hi Alan,
Can you please send the the command line that you used to generate the results, 
and a listing of the files in the mri directory of any subject you’ve analyzed?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 22 Nov 2016, at 16:48, Alan Francis 
> wrote:

Hi Eugenio -

Hope all is well with you at UCL. I have the run the subfields algorithm on a 
set of subjects using Freesurfer 6.0. All the brains were processed without 
much fuss. However, when I ran the following:

quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt

It yielded nothing.

Can you please help me?

Thanks,

Alan

--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
___
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.

[Freesurfer] quantifyHippocampalSubfields.sh

[Alan Francis]

Hi Eugenio -

Hope all is well with you at UCL. I have the run the subfields algorithm on
a set of subjects using Freesurfer 6.0. All the brains were processed
without much fuss. However, when I ran the following:

quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt

It yielded nothing.

Can you please help me?

Thanks,

Alan

-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
___
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] Fwd: recon-all -s Prueba2 exited with ERRORS

[Z K]

Hello,

This is a known issue with ubuntu16 platforms and other distributions 
that include perl 5.22. That version of perl is incompatible with the 
version of the mni tools shipped with freesurfer 5.3

The issue has been fixed in the freesurfer v6-beta release 
(https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall6.0-beta) 
and the upcoming v6 release.

Additionally, you can use perlbrew to downgrade your version of perl to 
v5.20



On 11/21/2016 06:34 PM, Gabriela De Pino wrote:
> Hello FreeSurfer Developers,
>
> I'm attempting to compute autorecon1 and everything goes well until 
> mri_nu_correct.mni, where I get the following error:
>
>
>
> /usr/local/freesurfer/subjects/Prueba2/mri
>
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
> orig.mgz --o orig_nu.mgz
>
> Linux HULK 4.4.0-47-generic #68-Ubuntu SMP Wed Oct 26 19:39:52 UTC 2016 
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s Prueba2 exited with ERRORS at lun nov 21 19:27:17 ART 2016
>
> For more details, see the log file 
> /usr/local/freesurfer/subjects/Prueba2/scripts/recon-all.log
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> 2) Platform: Ubuntu 16.04.1 LTS (Xenial Xerus)
>
> Thank you very much! Bets regards,
>
> Gabriela
>
>
>
>
> ___
> 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] mris_make_surfaces - longitudinal stream - questions

[Martin Reuter]

Hi Antonin, 

I had answered that in my email from Nov. 18.. 

Thickness is not constrained to 3.5mm, but see my email for the full answer.

Best, Martin


> On Nov 22, 2016, at 12:15 PM, Antonin Skoch  wrote:
> 
> Dear experts,
> 
> I am trying to understand what is the specificity of the pial and white 
> surface generation in longitudinal stream, i.e. how the information from 
> processing of base template is used for surface estimation in -long step of 
> recon-all.
> 
> Specifically:
> Why the maximal thickness is constrained to 3.5 mm (default in 
> cross-sectional stream is 5 mm)?
> 
> What is precisely the significance of -long parameter of mris_make_surfaces?
> In the source code is written, that this directive resets starting position 
> of pial surface to be slightly inside the orig_pial.
> What is the objective of this step?
> 
> Regards,
> 
> Antonin Skoch
> 
> ___
> 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] Longitudinal stream : LME and limits of model

[Martin Reuter]

Hi Matthieu, 
(also inline)

> On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte 
>  wrote:
> 
> Hi Martin,
> 
> Thanks for replying. Please see inline below:
> 
>> Le 21 nov. 2016 à 20:26, Martin Reuter > > a écrit :
>> 
>> Hi Matthieu, 
>> 
>> a few quick answers. Maybe Jorge knows more. 
>> Generally number of subjects / time points etc. cannot be specified 
>> generally. All depends on how noisy your data is and how large the effect is 
>> that you expect to detect. You can do a power analysis in order to figure 
>> out how many subject / time points would be needed. There are some tools for 
>> that in the LME toolbox:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#Poweranalysis
>>  
>> 
>>  
>> 
>> 1. see above
>> 2. yes, also time points can miss from the middle. If you have mainly 
>> missing time points at the end, this will bias your analysis to some extend, 
>> as the remaining ones may be extremely healthy, as probably the more 
>> diseased ones drop out. You may want to do a time-to-event (or 
>> survival-analysis) which considers early drop-out.
> 
> Is there any way to do with Freesurfer this kind of analysis ?

https://surfer.nmr.mgh.harvard.edu/fswiki/SurvivalAnalysis 
 
Yes, there is also a paper where we do this. It is a combination of LME and 
Survival Analysis (as for the SA you need to have measurements of all subjects 
at all time points, so you estimate that from the LME model). 

> 
>> 3. see above (power analysis)
>> 4. GIGO means garbage in, garbage out, so the less you QC, the more likely 
>> will your results be junk. The more you QC the less likely will it be junk, 
>> but could still be. The FS wiki has lots of tutorial information on checking 
>> freesurfer recons. For longitudinal, you should additionally check the 
>> surfaces in the base, the brain mask in the base, and the alignment of the 
>> time points (although there is some wiggle space for the alignment, as most 
>> things are allowed to evolve further for each time point). 
> 
> For the alignment of the time points, should I better comparing brainmask or 
> norm.mgz ?

It does not really matter, I would use norm.mgz. I would load images on top of 
each other and then use the opacity slider in Freeview to blend between them 
(that way the eye can pick up small motions). I would not worry too much about 
local deformations which could be caused by non-linearity (gradient). But if 
you see global misalignment (rotation, translation) it is a cause for concern) .

> 
> In order to avoid bias by adding further time points in the model by the -add 
> recon all command, is this better for each subject to take into account all 
> the time points existing for it or only the ones that I will include in the 
> model (three time points / subject ; if existing 6 time points for any 
> subject ?)
> 

Usually it is recommended to run all time points in the model (so a base with 6 
time points) and not use the - - add flag. Also, Linear Mixed Effects models 
deal well with missing time points. It is perfectly OK to have differently many 
time points per subject for that. You should still check if there is a bias 
(e.g. one group always has 3 time points the other 6) that would not be good. 
Maybe also consult with a local biostatistician if you are not comfortable with 
the stats. The LME tools are matlab, and so are the survival-analysis scripts. 

Best, Martin



> Best regards,
> Matthieu
> 
>> 
>> Best, Martin
>> 
>>> On Nov 21, 2016, at 7:07 PM, Matthieu Vanhoutte 
>>> > wrote:
>>> 
>>> Dear Freesurfer’s experts,
>>> 
>>> I would have some questions regarding the LME model to be used in 
>>> longitudinal stream:
>>> 
>>> 1) Which are the ratio limits or % of missing timepoints accepted ? 
>>> (according time, I have less and less subjects time points)
>>> 
>>> 2) Is it possible to include patients that would miss the first timepoint 
>>> but got the others ?
>>> 
>>> 3) Considering a group in longitudinal study, which is the number of 
>>> subjects minimal of this group accepted for LME modeling ?
>>> 
>>> 4) Finally, concerning quality control and among a big number of total time 
>>> points, which essential controls are necessary ? (Control of norm.mgz of 
>>> the base, alignment of longitudinal timepoints on base,… ?)
>>> 
>>> Best regards,
>>> Matthieu
>>> 
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>> 
>>> 
>>> 
>> 
>> 

Re: [Freesurfer] Fwd: [HCP-Users] HCP to FreeSurfer Resampling

[Bruce Fischl]

Hi Tim

we need your full command line and screen output.

cheers
Bruce
On Tue, 22 Nov 2016, 
Timothy Hendrickson wrote:

> 
> Just following up on the message below.
> 
> Respectfully,
> 
> -Tim 
> 
> FreeSurfer experts,
> 
> I am attempting to resample HCP data into FreeSurfer space with the
> following how to document: https://wiki.humanconnectome.
> org/display/PublicData/HCP+Users+FAQ.
> 
> I believe I have resampled the GIFTI file into fs_average space, however I
> am running to problems visualizing it in freeview or tksurfer. Please see
> the error message in the forwarded message below?
> 
> -Tim
> 
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434 (texts okay)
> 
> -- Forwarded message --
> From: Timothy Hendrickson 
> Date: Tue, Nov 8, 2016 at 8:51 AM
> Subject: Re: [HCP-Users] HCP to FreeSurfer Resampling
> To: Timothy Coalson 
> Cc: "hcp-us...@humanconnectome.org" 
> 
> 
> Hi Tim,
> 
> Thank you for taking a look at my script, I really appreciate it. I am now
> running into another problem. After re-sampling into fs_average space I am
> attempting to visualize that file as an overlay in tksurfer or freeview
> (freesurfer visualization tools) however I receive the following
> error: *mriseadGIFTIfile:
> mris is NULL! found when parsing file rh.43242.32k_TJH_fsavg.func.gii*. I
> know that freesurfer can handle GIFTI file so that is not the problem. I
> wonder if the GIFTI file was created incorrectly...
> 
> Any advice?
> 
> -Tim
> 
> 
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434 (texts okay)
> 
> __
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Office: 612-624-6441
> Mobile: 507-259-3434 (texts okay)
> 
>
___
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] Fwd: [HCP-Users] HCP to FreeSurfer Resampling

[Timothy Hendrickson]

Just following up on the message below.

Respectfully,

-Tim



FreeSurfer experts,

I am attempting to resample HCP data into FreeSurfer space with the
following how to document: https://wiki.humanconnectome.
org/display/PublicData/HCP+Users+FAQ.

I believe I have resampled the GIFTI file into fs_average space, however I
am running to problems visualizing it in freeview or tksurfer. Please see
the error message in the forwarded message below?

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)

-- Forwarded message --
From: Timothy Hendrickson 
Date: Tue, Nov 8, 2016 at 8:51 AM
Subject: Re: [HCP-Users] HCP to FreeSurfer Resampling
To: Timothy Coalson 
Cc: "hcp-us...@humanconnectome.org" 


Hi Tim,

Thank you for taking a look at my script, I really appreciate it. I am now
running into another problem. After re-sampling into fs_average space I am
attempting to visualize that file as an overlay in tksurfer or freeview
(freesurfer visualization tools) however I receive the following
error: *mriseadGIFTIfile:
mris is NULL! found when parsing file rh.43242.32k_TJH_fsavg.func.gii*. I
know that freesurfer can handle GIFTI file so that is not the problem. I
wonder if the GIFTI file was created incorrectly...

Any advice?

-Tim


Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)

__

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
___
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] how does the content of the curv files compare to that of smoothwm.H.crv

[Bruce Fischl]

Hi Fabio

I'll cc Rudolph who has worked with the curvature much more than I have, 
but some points:


1. The negative gyral/positive sulcal curvature is a consequence of 
adopting an outwards pointing surface normal direction.


2. I think the smoothwm.H.crv is generated from the ?h.smoothwm surface, 
while the ?h.curv is generated from the white. You could generate the 
equivalent for the white if you wanted.


3. We have 2 different ways of computing curvature. One fits a Hessian to 
the local height function in the tangent bundle (used in ?h.curv). The 
other is a discrete method, which I think is used in the smoothwm.H.crv, 
but Rudolph will know.


4. You can load the ?h.curv files in freeview or tksurfer and verify their 
appearance.


cheers
Bruce


On Tue, 22 Nov 2016, Bernardoni, Fabio wrote:


Dear Freesurfer experts,

I am having troubles interpreting the output of the recon-all output concerning 
the curvature, in particular in relation with the one from the command 
mris_curvature_stats.
My aim is to compare the absolute value of both the gaussian/intrinsic and the mean/extrinsic curvatures between a group of patients and a group of controls. In particular  I would like to obtain a voxelwise statistical maps for the comparison. 


Browsing the freesurfer mailing list I understood the following (please correct 
me if I am wrong):
- the file $SUBJECTS_DIR//surf/lh.smoothwm.H.crv, produced by 
mris_curvature_stats, contains the mean/extrinsic curvature map for the left hemisphere, as 
computed on the white matter surface, for subject 
- the file $SUBJECTS_DIR//surf/lh.curv, produced by recon-all (or by mris_curvature, right?) contains a smoothed version of smoothwm.H.crv 
- the files $SUBJECTS_DIR//surf/lh.pial.H.crv and $SUBJECTS_DIR//surf/lh.curv.pial are the analogues of the above, but for the pial surface


Also the local gyrification index, contained in the file$SUBJECTS_DIR//surf/lh.pial_lgi, is 
computed  on the pial surface and might be compared (I know it is a different measure) with 
$SUBJECTS_DIR//surf/lh.pial.H.crv and $SUBJECTS_DIR//surf/lh.curv.pial, not with  
$SUBJECTS_DIR//surf/lh.curv or $SUBJECTS_DIR//surf/lh.smoothwm.H.crv.

If this is true I expect that: 
1- the histograms of the above quantities for any subject be approximately symmetric around zero. Actually given that the convention chosen is to give a positive curvature to the suci and a negative to the gyri (also read in one email of this list from long time ago - so please correct me if I am wrong), I expect that the mean value would lie a bit below zero if we want the brain surface to close (with this convention a sphere has mean curvature -1/r). This expectation of mine is only a rough expectation, but it would be precise if one had normalized somehow for the area related to the vertex on which the local curvature is computed. 
2- the histograms for   smoothwm.H.crv and  pial.H.crv would have fatter tails than curv and curv.pial, respectively

3-  smoothwm.H.crv and  pial.H.crv would follow quite closely curv and 
curv.pial, respectively, for each subject

Now please have a look at the attached plots, where in red always appear 
unsmoothed quantities, while in blue smoothed ones. NB I have extracted the 
above plotted values using the functions fs_read_Y from the freesurfer  
longitudinal package by M. Reuter et al.

Now I observe that 1,2,3 are true on the white matter surface (see attached 
*smoothwm* files). Also, if I average the mean curvature for one subject over 
all vertices I obtain a negative value. When I look at the analogue plots for 
the pial surface2,3 are still true, but the mean values for the curvatures are 
now positive!
If I look at the  *pial* files, the distribution looks clearly different.

Therefore I have the following doubts/questions:
a) is the convention for the curvature sign different on the pial and on the wm 
surface?
b) if not, can the normalization issue I mention in point 1 above explain the  
negative mean of the mean-curvature I observe (the subject I used to produce 
the plots is a healthy control, plots are similar for other subjects)?
c) in any case I expected the survatures to be more similar to each other on 
the wm and on the pial surface, given that they are approximately parallel. Any 
comment on this would be highly appreciated.
d) or do you think my results are wrong/ I am not plotting the right thing?


Thanks in advance for any help. 


Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter
Psychosoziale Medizin und Entwicklungsneurowissenschaften
Tel. +49 (0)351 458-5245
Fax +49 (0)351 458-7206
URL http://www.uniklinikum-dresden.de/psm; www.transdenlab.de
Universitätsklinikum Carl Gustav Carus & Medizinische Fakultät
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des 

[Freesurfer] mris_make_surfaces - longitudinal stream - questions

[Antonin Skoch]

Dear experts,

I am trying to understand what is the specificity of the pial and white surface 
generation in longitudinal stream, i.e. how the information from processing of 
base template is used for surface estimation in -long step of recon-all.

Specifically:
Why the maximal thickness is constrained to 3.5 mm (default in cross-sectional 
stream is 5 mm)?

What is precisely the significance of -long parameter of mris_make_surfaces?
In the source code is written, that this directive resets starting position of 
pial surface to be slightly inside the orig_pial.
What is the objective of this step?

Regards,

Antonin Skoch

___
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.