[Freesurfer] myelin analysis with cortical thickness pvr

[Damien MARIE]

External Email - Use Caution

Hi,

I would like to replicate an analysis I did with qdec but regressing out 
thickness at the vertex level. It’s a myelin group difference with age and left 
average myelin as nuisance factors.

I used the mri_glmfit command line generated during that qdec analysis and  
added the pvr flag but I got that error message:

ERROR: dimension mismatch between X and contrast 
/home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat
   X has 7 cols, C has 6 cols

I understood I had to change the contrast.mat and added a 0 at the end for the 
pvr: +1.0 -1.0 +0.0 +0.0 +0.0 +0.0 +0.0 

Can you please tell me if it is correct??? I would like to be sure.

I see more or less the same results than before except that some clusters are a 
bit degraded let say, as if I was working with a lower level of smoothing.

Damien 

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[Freesurfer] myelin group difference and pvr of thickness

[Damien MARIE]

External Email - Use Caution

Hi,

I would like to replicate an analysis I did with qdec but regressing out  
thickness at the vertex level. It’s a myelin group difference with age and left 
average myelin as nuisance factors.

Q1/ should I use smoothed thickness maps or unsmoothed?



I used the mri_glmfit command line generated during that qdec analysis and 
added the pvr flag but I got that error message:

ERROR: dimension mismatch between X and contrast 
/home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat
   X has 7 cols, C has 6 cols

I understood I had to change the contrast.mat and added a 0 at the end for the 
pvr: +1.0 -1.0 +0.0 +0.0 +0.0 +0.0 +0.0 

Q2/ Can you please tell me if it is correct???


Many thanks,

Damien





fsgd:
GroupDescriptorFile 1
Title 10nov
MeasurementName R1projfrac0.5
Class group1
Class group2
Variables LH_mR1 Age 
Input suj1 group1 0.080687 1.64
…

glm:
mri_glmfit --y /home/damien/bin/freesurfer6/subjects/qdec/10nov/y.mgh —fsgd 
/home/damien/bin/freesurfer6/subjects/qdec/10nov/qdec.fsgd dods --glmdir 
/home/damien/bin/freesurfer6/subjects/qdec/10nov --surf fsaverage lh —label 
/home/damien/bin/freesurfer6/subjects/fsaverage/label/lh.aparc.label --C 
/home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat
 --C 
/home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Diff-ct-dys-Intercept-R1projfrac0.5.mat
 --pvr lh.thicknessall.fsaverage.mgh 



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[Freesurfer] myelin and thickness pvr

[Damien MARIE]

External Email - Use Caution

Dear freesurfer experts,

I would like to replicate an analysis I did with qdec but regressing out 
thickness at the vertex level. It’s a myelin group contrast with age and left 
average myelin as nuisance factors.

I used the mri_glmfit command line generated during that qdec analysis and 
added the pvr flag but I got that error message:

ERROR: dimension mismatch between X and contrast 
/home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat
   X has 7 cols, C has 6 cols

How can I solve that, should I modify the contrast.mat?

Many thanks,

Damien

mri_glmfit --y /home/damien/bin/freesurfer6/subjects/qdec/10nov/y.mgh --fsgd 
/home/damien/bin/freesurfer6/subjects/qdec/10nov/qdec.fsgd dods --glmdir 
/home/damien/bin/freesurfer6/subjects/qdec/10nov --surf fsaverage lh --label 
/home/damien/bin/freesurfer6/subjects/fsaverage/label/lh.aparc.label --C 
/home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat
 --C 
/home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Diff-ct-dys-Intercept-R1projfrac0.5.mat
 --pvr lh.thicknessall.fsaverage.mgh 



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Re: [Freesurfer] Myelinated cortical thickness ratio map

[Damien MARIE]

External Email - Use Caution

Hi Matt,

Many thanks for your prompt reply, you are right.

Any tips on how I could do that?

Should I regress out cortical thickness from my myelin maps at the individual 
level, save the individual output myelin maps and run analyses on the latter? 
If yes how?

That’s really important to me otherwise a reviewer could claim the myelin 
differences we detect might be supported by cortical thickness variations and 
not myelin…

Thank you and best,

Damien



> Glasser, Matthew 
> <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Glasser%2C+Matthew%22>
>  Mon, 22 Oct 2018 12:57:43 -0700 
> <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20181022>
> 
> Regression would be better than division.
> Matt.
> 
> From: 
>  <http://nmr.mgh.harvard.edu/><mailto:freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>>
>  on behalf of Damien MARIE http://damien.ma/>...@unige.ch 
> <http://unige.ch/><mailto:damien.ma...@unige.ch 
> <mailto:damien.ma...@unige.ch>>>
> Reply-To: Freesurfer support list 
>  <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> Date: Monday, October 22, 2018 at 8:54 AM
> To: "freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>" 
>  <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> Subject: [Freesurfer] Myelinated cortical thickness ratio map
> 
> 
> External Email - Use Caution
> 
> Dear experts,
> 
> I am working with R1 maps that I project on the surface. The goal is to look 
> at 
> intra-cortical myelin.
> 
> I detect interesting effects between two groups. Now I would like to compute 
> myelinated cortical thickness ratio maps, in order to control for the effect 
> of 
> cortical thickness variations occurring with gyrification.
> 
> Here is a paper where they describe a way to compute those myelinated 
> cortical 
> thickness ratio map with MIPAV and the MPI-CBS toolbox : 
> https://www.ncbi.nlm.nih.gov/pubmed/29321232 
> <https://www.ncbi.nlm.nih.gov/pubmed/29321232>
> «  The proportional thickness of the myelinated part of the cortex in 
> relation 
> to its overall thickness (myelinated cortical thickness) was computed with a 
> fuzzy classification technique combining information about radial and 
> tangential fibers.  «
> 
> 1- Is it possible to do the same in FreeSurfer?
> 
> 2- What about dividing my individual myelin maps by the individual cortical 
> thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do 
> the job in the volume but I don’t know how I could do that in FreeSurfer.
> 
> Any comments / other suggestions are welcome.
> 
> Thank you and best,
> 
> Damien
> 

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[Freesurfer] Myelinated cortical thickness ratio map

[Damien MARIE]

External Email - Use Caution

Dear experts,

I am working with R1 maps that I project on the surface. The goal is to look at 
intra-cortical myelin.

I detect interesting effects between two groups. Now I would like to compute 
myelinated cortical thickness ratio maps, in order to control for the effect of 
cortical thickness variations occurring with gyrification.  

Here is a paper where they describe a way to compute those myelinated cortical 
thickness ratio map with MIPAV and the MPI-CBS toolbox : 
https://www.ncbi.nlm.nih.gov/pubmed/29321232 

«  The proportional thickness of the myelinated part of the cortex in relation 
to its overall thickness (myelinated cortical thickness) was computed with a 
fuzzy classification technique combining information about radial and 
tangential fibers.  « 

1- Is it possible to do the same in FreeSurfer?

2- What about dividing my individual myelin maps by the individual cortical 
thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do 
the job in the volume but I don’t know how I could do that in FreeSurfer.

Any comments / other suggestions are welcome.

Thank you and best,

Damien
 
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[Freesurfer] glm results : opposite direction between whole-brain analysis and feature extraction in the significant clusters

[Damien MARIE]

Hi,

I am working on R1 maps. I ran a very simple glm on smoothed R1 maps, FWHM = 8 
mm, population 1, population 2 , and age as nuisance factor.

After POS MC simulation CW correction, I had two significant clusters resulting 
from this in the planum temporale and Heschl’s sulcus. The contrast being 
population 1 - population 2, my interpretation was higher R1 values in these 
two clusters in Pop 1 as compared to Pop 2.

After that I wanted to run some post-hoc tests let say, in a statistical 
software similar to SPSS, JMP, on the mean R1 values from each of these 
clusters. 

The strategy I picked was to stay in the common space, fsaverage, and apply 
mri_segstats:


#Extract mean R1 in montecarlo's significantcluster 

for i in `cat subjects`
do mri_segstats --mul 1000 --annot fsaverage lh PT_mc-z.pos.sig.ocn --i 
$SUBJECTS_DIR/${i}/surf/lh.R1.fsaverage.fwhm8.mgh --sum lh.PT.R1.${i}.stats
done

for i in `cat subjects`
do mri_segstats --mul 1000 --annot fsaverage lh HS_mc-z.pos.sig.ocn --i 
$SUBJECTS_DIR/${i}/surf/lh.R1.fsaverage.fwhm8.mgh --sum lh.HS.R1.${i}.stats
done



Everything when fine but as compared to my glm analysis when looking at mean 
group differences in my stat software I have the opposite  : larger R1 values 
in Pop 2 as compared to Pop 1 (after removing the effect of age or not, and 
removing one outlier or not).

I went back to my glm and checked everything, fsgd file, matrix and so on, 
everything seems ok I am not mistaken on the direction of my glm contrast (pop 
1 - pop 2) so I do not get it at all.

Any advices?

For now I am thinking about going back in the individual space, registering my 
clusters in the individual surfaces (label2surf something like that) and then 
extract my mean R1 values, or  extract values in non-smoothed maps, but I do 
not think it will change anything.


Damien



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[Freesurfer] Average hemispheric R1 value

[Damien MARIE]

Dear experts,

I would like to extract the mean left / right R1 value for each of my subjects 
(R1 = 1/T1). I did that with mris_anatomical_stats (see below) and I’m assuming 
that “ average cortical thickness = 0.001 mm +- 0.000 mm “ is my average R1 
value (in that case for the right hemi). Is that correct?

Now I would like to get my average hemi R1 value with 5 decimal numbers if 
possible because R1 values are very low, for instance in the same subject 
considering the whole brain average R1 is equal to 0.000737 . Is it possible ?

Thank you and best,

Damien



mris_anatomical_stats -t rh.R1.mgh ct_pp2_N4_bet_MP2RAGEcorr rh
outputting results to R1file...
using thickness file rh.R1.mgh.
reading volume 
/home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/mri/wm.mgz...
reading input surface 
/home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.white...
Using TH3 vertex volume calc
Total face volume 293919
Total vertex volume 289553 (mask=0)
reading input pial surface 
/home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.pial...
reading input white surface 
/home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.white...
structure is 
"/home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.white"
number of vertices  = 148874
total surface area  = 103857 mm^2
total gray matter volume= 289553 mm^3
average cortical thickness  = 0.001 mm +- 0.000 mm
average integrated rectified mean curvature = 0.136
average integrated rectified Gaussian curvature = 0.030
folding index   = 2174
intrinsic curvature index   = 190.6



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[Freesurfer] mean hemispheric value in a .mgh

[Damien MARIE]

Hi,

I’ve a .mgh that is a volume projected on the surface of the same subject at 
mid-thickness (output of mri_vol2surf) .

I would like to extract the mean hemipheric value in this X.mgh.

I guess it is possible with mris_anatomical stats but probably my command line 
is incorrect (see below).

Any advices?

Thank you and best,

Damien



mris_anatomical_stats ct_pp1_N4_bet_MP2RAGEcorr -a 
ct_pp1_N4_bet_MP2RAGEcorr/label/lh.aparc.annot lh R1.mgh 

computing statistics for each annotation in 
ct_pp1_N4_bet_MP2RAGEcorr/label/lh.aparc.annot.
reading volume 
/home/damien/bin/freesurfer6/subjects/ct_pp1_N4_bet_MP2RAGEcorr/mri/wm.mgz...
reading input surface 
/home/damien/bin/freesurfer6/subjects/ct_pp1_N4_bet_MP2RAGEcorr/surf/lh.R1.mgh...
ERROR: MRISread: file 
'/home/damien/bin/freesurfer6/subjects/ct_pp1_N4_bet_MP2RAGEcorr/surf/lh.R1.mgh'
 has 0 vertices!
Probably trying to use a scalar data file as a surface!


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[Freesurfer] Looking for advices on the best parameters to use with a Montecarlo cluster-wise correction

[Damien MARIE]

Hi,

I would like to get your opinion about Montecarlo statistics. I know that there 
is maybe not a simple answer and that it depends probably on the research 
question but anyway, is there some kind of gold standard about the number of 
montecarlo simulations / p values ?

Speaking about that with colleagues, I had plenty of divergent opinions for 
both variables depending on their neuroimaging field i.e minimum 10,000 / 3,000 
/ 1,000 simulations - minimum p < 0.05 / 0.001 (the latest threshold being 
advised on the basis on the recent papers on false positives) .

I am also wondering if it makes sense to use this correction as a "SPM-like 
small volume correction".

What I mean by SPM-like small volume correction, is when you got clusters in a 
region for which you have an apriori hypothesis, that they do not survive to 
multiple comparisons, and you restrain your analysis to the region of interest. 
In my study, it would be 1 or 2 merged labels from the auditory cortex.

Thank you for your input,

Best,

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[Freesurfer] mri_mcsim update and FreeSurfer6

[Damien MARIE]

I just read this statement : “ A newer version of mri_mcsim for linux can be 
obtained from here: 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_mcsim.linux
 
<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_mcsim.linux>
 Copy it to $FREESURFER_HOME/bin/mri_mcsim “ here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo 
<https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo>

I am working with FreeSurfer6, should I update it or it was implemented in the 
version 6?

Thank you and best,

Damien MARIE


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Re: [Freesurfer] Any advices for hires surface reconstruction?

[Damien MARIE]

Hi,

Thank you for your reply Douglas, I will talk with my supervisor about an 
eventual contribution.

Best,

Damien








Douglas Greve 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+Greve%22>
 Tue, 18 Apr 2017 18:41:59 -0700 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20170418>
That looks pretty good to me considering the resolution and 7T. We will be 
re-evaluating the hires stream over the next year. If you want to contribute a 
problem data set to our test suite, that would be appreciated.
doug

On 4/17/17 1:45 PM, Damien MARIE wrote:
Hi,

I have a project on 7T data. I processed 26 subjects with FreeSurfer6 recon-all 
with or without the hires flag. The input is MP2RAGE, 0.6 mm^3, bias corrected, 
skull strip was done despite a slight piece of dura is still present.
For the data processed at native resolution, with the hires flag, I mainly used 
this: recon-all -subject -i -parallel -expert -hires
The expert file indicating only mris_inflate -n 50
As a result, skull strip had to be fixed for 5 subjects (missing brain pieces). 
Bilateral temporal pole is missing in the reconstructed surfaces in 19 subjects.
For the downsampled data, without the hires flag : recon-all -subject -i 
-parallel Bilateral temporal pole is missing in the reconstructed surfaces in 
only 1 subject. Surfaces are way smoother.
I guess such differences between the classic pipeline and the pipeline tuned 
for hires data are expected. I was just wondering if I was missing something 
somewhere, some additional options that I would need to tweak, to get better 
surfaces with the hires data especially in the temporal pole. For now the only 
things I see that I could do are adding checkpoints or play with this command 
line: mris_make_surfaces -max_gray_at_csf_border X -max_csf Y
Thank you and best,

*Damien*

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[Freesurfer] Any advices for hires surface reconstruction?

[Damien MARIE]

Hi,

I have a project on 7T data. I processed 26 subjects with FreeSurfer6 recon-all 
with or without the hires flag. The input is MP2RAGE, 0.6 mm^3, bias corrected, 
skull strip was done despite a slight piece of dura is still present.

For the data processed at native resolution, with the hires flag, I mainly used 
this: recon-all -subject -i -parallel -expert -hires
The expert file indicating only mris_inflate -n 50
As a result, skull strip had to be fixed for 5 subjects (missing brain pieces). 
Bilateral temporal pole is missing in the reconstructed surfaces in 19 
subjects. 

For the downsampled data, without the hires flag : recon-all -subject -i 
-parallel
Bilateral temporal pole is missing in the reconstructed surfaces in only 1 
subject. Surfaces are way smoother.

I guess such differences between the classic pipeline and the pipeline tuned 
for hires data are expected.
I was just wondering if I was missing something somewhere, some additional 
options that I would need to tweak, to get better surfaces with the hires data 
especially in the temporal pole. For now the only things I see that I could do 
are adding checkpoints or play with this command line: mris_make_surfaces 
-max_gray_at_csf_border X -max_csf Y

Thank you and best,

Damien

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[Freesurfer] ERROR

[Damien MARIE]

Hi,

Just a follow-up about the message I posted. Problem is solved. I just moved 
freesurfer/ outside of the Applications folder (from 
/Users/me/Applications/freesurfer to /Users/me/freesurfer ).

So now I can work with my macbook on subjects previously processed with another 
system. Probably an issue with mac os (10.11.6 ?) and copy pasting files in a 
subdirectory of the Applications folder… 

Thanks,

Damien

___

Damien MARIE 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Damien+MARIE%22>
 Sat, 15 Apr 2017 06:22:31 -0700 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20170415>
Hi,

I ran recon-all on a server where Ubuntu is running.
Recently I installed separately freesurfer on a macbook, it is working (e.g. 
tkmedit bert), I moved my processed subjects to freesurfer/subjects on the 
macbook but I can not work with them. I have the below error. I changed the 
permission to 777, it is still not working. Now what is really strange is that, 
using the finder I do not see the files in freesurfer/subjects but by doing ls 
-l in a terminal, I can see them…

Please note that SUBJECT_DIR is defined.

Any idea is welcome.

Thank you and best,


Damiens-MacBook-Pro-2:subjects dmarie2$ tkmedit 
hires_ct_pp1_N4_bet_MP2RAGEcorr/ brainmask.mgz -aux T1.mgz
ERROR: cannot find subject hires_ct_pp1_N4_bet_MP2RAGEcorr/ in 
/Applications/freesurfer/subjects or it is not readable by you


Damien 
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[Freesurfer] ERROR

[Damien MARIE]

Hi,

I ran recon-all on a server where Ubuntu is running.

Recently I installed separately freesurfer on a macbook, it is working (e.g. 
tkmedit bert), I moved my processed subjects to freesurfer/subjects on the 
macbook but I can not work with them. I have the below error. I changed the 
permission to 777, it is still not working. Now what is really strange is that, 
using the finder I do not see the files in freesurfer/subjects but by doing ls 
-l in a terminal, I can see them…

Please note that SUBJECT_DIR is defined.

Any idea is welcome.

Thank you and best,


Damiens-MacBook-Pro-2:subjects dmarie2$ tkmedit 
hires_ct_pp1_N4_bet_MP2RAGEcorr/ brainmask.mgz -aux T1.mgz
ERROR: cannot find subject hires_ct_pp1_N4_bet_MP2RAGEcorr/ in 
/Applications/freesurfer/subjects or it is not readable by you


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Re: [Freesurfer] Quantifying volumes

[Damien MARIE]

Hi,

Just adding a word about the e-mail of ma colleague Josue. What he meant is 
that he extracted volumes for exactly the same ROI (a merging of destrieux 
labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv 
file of this ROI, mri_binarize and mri_segstats  or 2- a .label file of this 
ROI and mris_anatomical_stats.

We get a different volume output (ratio of difference between the 2 methods = 
approx. 2.5, similar to mean thickness I would say…), so we would like to 
understand what is happening exactly. 

Using the method 1, it’s actually a surface measurement we get no?

Would that be possible to convert a .cuvr file to a .label file ?

Thank you and best,
Damien


Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700
Dear Doug,

Thank you very much for your advice!
We get to extract results for the volumes from a ".curv file encoded ROI" using 
your recommended command lines (mri_binarize and mri_segstats ), but 
unfortunately the results are much smaller (around 3 times) than when we 
extract total gray matter volumes from a respective ".label file encoded ROI" 
using mris_anatomical_stats .
Example:
Volumes from a ".curv file encoded ROI" using your recommended command lines 
(mri_binarize and mri_segstats):
Subject1 = 1090
Subject2 = 1181
Subject3 = 713
Subject4 = 1230
Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats):
Subject1 = 3497
Subject2 = 3786
Subject3 = 2268
Subject4 = 3491

Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize 
and mri_segstats) an estimation of the total gray matter volumes?
Why these values are differing that much?

Thank you very much,
Josue Dalboni

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

Sent: Wednesday, October 5, 2016 5:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Quantifying volumes

I would binarize the curv file with

mri_binarize --i lh.yourcurvfile --abs --min .001 --o
lh.yourcurvfilebin.mgh

Then compute the volume with

mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume
--accumulate --sum lh.vol.yourcurv.sum


On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
> Dear Douglas,
>
> I have a ".curv" file that contains the curvature information inside an 
> automatically delineated ROI and 0 everywhere else.
> I would like to calculate the volume of this ROI,
>
> Can I extract statistics directly from the ".curv" file?
>
> Best regards,
> Josue
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Tuesday, October 4, 2016 9:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Quantifying volumes
>
> What is the nature of the segmentation? Is it just a binary (1=in,
> 0=out) segmentation? And what file format? In general we don't use .w
> anymore, but it can be converted into something else.
>
> doug
>
>
> On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
>> Dear Douglas,
>>
>>
>> I have a segmented gyrus curvature file (.curv or .w) and I would like
>> to calculate the volume (and other statistics) of this gyrus.
>>
>>
>> I currently only know mris_anatomical_stats to perform that, but
>> requiring a '.label' file.
>>
>>
>> Can I extract statistics directly from the ".curv" file?
>>
>>
>> Or can I convert directly from .curv to .label in order to extract
>> these statistics?
>>
>>
>> As another option, is it feasible to convert the '.curv' file to nifti
>> volume (mri_surf2vol), binarize it (mri_binarize), and then convert to
>> label (mri_cor2label)?
>>
>>
>> What does the output nifti file from 'mri_surf2vol' contain? Does it
>> contain the complete volume behind the surface? Or does it only
>> contain the surface over the 3D space?
>>
>>
>> Thank you very much in advance for your help!
>>
>>
>> Best regards,
>>
>> Josue
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> 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 

Re: [Freesurfer] FreeSurfer 6 beta and mac osx el capitan

[Damien MARIE]

Hi,

I downloaded the archive with Firefox instead of Safari and problem is solved. 
Strangely, the archive downloaded with Safari was not full.

Damien 

> On 10 Oct 2016, at 16:56, Damien MARIE <damien.ma...@unige.ch> wrote:
> 
> Hi,
> 
> I would like to install the FreeSurfer 6 beta on my macbook pro (OS X El 
> capitan 10.11.6, XQuartz 2.7.9 installed).
> 
> I allowed applications downloaded from Anywhere in privacy and settings, and 
> disabled csrutil (the System Integrity Protection, a security feature that 
> hobbles some of the capabilities of root since this OS release). No matter 
> what I try,  I cannot decompress the archive.
> 
> Using the terminal and sudo : 
> tar: Error opening archive: Failed to open 
> '/Users/dmarie2/Applications/freesurfer-Darwin-OSX-dev.tar.gz’
> 
> Or by double clicking :
> Unable to expand “freesurfer-Darwin-OSX-dev.tar.gz (Error 1 - Operation not 
> permitted).
> 
> I was wondering if somebody experienced this issue and would eventually have 
> a solution.
> 
> Thank you and best,
> 
> Damien

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[Freesurfer] FreeSurfer 6 beta and mac osx el capitan

[Damien MARIE]

Hi,

I would like to install the FreeSurfer 6 beta on my macbook pro (OS X El 
capitan 10.11.6, XQuartz 2.7.9 installed).

I allowed applications downloaded from Anywhere in privacy and settings, and 
disabled csrutil (the System Integrity Protection, a security feature that 
hobbles some of the capabilities of root since this OS release). No matter what 
I try,  I cannot decompress the archive.

Using the terminal and sudo : 
tar: Error opening archive: Failed to open 
'/Users/dmarie2/Applications/freesurfer-Darwin-OSX-dev.tar.gz’

Or by double clicking :
Unable to expand “freesurfer-Darwin-OSX-dev.tar.gz (Error 1 - Operation not 
permitted).

I was wondering if somebody experienced this issue and would eventually have a 
solution.

Thank you and best,

Damien
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Re: [Freesurfer] Processing 7T data

[Damien MARIE]

Hi,

Many thanks to all for your replies.

What do you mean by waiting Bruce, the version 6.0 could be soon released? 

Thank you and best,

Cheers, 

Damien






Bruce Fischl 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Bruce+Fischl%22>
 Thu, 06 Oct 2016 07:11:04 -0700 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20161006>
Hi Damein

6.0 beta will handle this *much* better if you can wait.
cheers
Bruce



> On 6 Oct 2016, at 15:46, Falk Lüsebrink <falk.luesebr...@ovgu.de> wrote:
> 
> Hi Damien,
> 
> depending on what you want to do you are forced to use the stable release. 
> The developmental version of FreeSurfer should be used for testing only, not 
> publishing results.
> 
> Following the notes of the HiResRecon 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon) you should be able to 
> process your data with version 5.1 and above at native resolution. However, 
> this affects the surfaces based processing only as the aseg.mgz is simply 
> upsampled from previously downsampled data. There are also a few methods to 
> make use of the native resolution which I haven't tested in recent past, e.g. 
> using the surface of the downsampled data on the native data. Otherwise you 
> will have to downsample you data to 1mm using v5.3.
> 
> Version 6 will be able to handle high resolution data at native resolution 
> using the -hires flag, making the workaround of the HiResRecon obsolete. 
> Having tested the developmental version (from mid September) on several high 
> resolution 7T datasets it seems to work nicely and is less laborious than 
> before. I haven't compared results between v5.3 and v6 though.
> 
> Best,
> Falk
> 
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Damien MARIE
> Gesendet: Donnerstag, 6. Oktober 2016 14:01
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: [Freesurfer] Processing 7T data
> 
> Dear experts,
> 
> I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is 
> to look a R1 maps.
> 
> I was wondering what was your opinion concerning the downsampling to 1 mm^3 
> (performed by the current FreeSurfer version if I am correct). What do you 
> think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or FreeSurfer 
> beta 6.0?
> 
> Thank You and Best,
> 
> Damien
> 
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> 
> 
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> addressed. If you believe this e-mail was sent to you in error and the e-mail 
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> at http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error but does not contain patient information, please contact the sender and 
> properly dispose of the e-mail.
> 

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[Freesurfer] Processing 7T data

[Damien MARIE]

Dear experts,

I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is 
to look a R1 maps.

I was wondering what was your opinion concerning the downsampling to 1 mm^3 
(performed by the current FreeSurfer version if I am correct). What do you 
think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or FreeSurfer beta 
6.0?

Thank You and Best,

Damien

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Re: [Freesurfer] REPOST cluster feature extraction from qdec output

[Damien MARIE]

Hi,

Many thanks for your prompt reply Pr. Greve.

I did :

mri_glmfit --y 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh 
--fsgd 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/qdec.fsgd
 dods --glmdir 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA --surf 
fsaverage rh --label 
/home/damien/bin/freesurfer/subjects/fsaverage/label/rh.aparc.label --C 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Avg-Intercept-area.mat
 --C 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Diff-dyslexic-control-Intercept-area.mat
 --C 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Diff-male-female-Intercept-area.mat
 --C 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-X-group-gender-Intercept-area.mat
 --eres-save

mri_segstats --in 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/eres.mgh 
--sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf 
RH_Dys-CT_CSA_AgeGenderWRCSA.dat


1) I don’t get it though. Probably I made a bad description of my goal, perhaps 
using this terminology of “residuals” also is not very accurate.

I exported the txt file (output of mri_segstats computed on eres.mgh) to a 
statistical software and ran a mancova per cluster on cluster values with 
covariatess : age, right hemispheric surface area + gender factor. I find 
significant effects of the covariates on 7/9 clusters.

I was not expecting such effects. I wanted to extract residuals of surface area 
in the significant clusters obtain using the Qdec Monte Carlo simulation on the 
contrast of interest (Dys - Ct) after removing all covariate effects.

My aim was to look at the differences between the two levels of the factor of 
interest to get a sense of what is happening in this Qdec analysis and this 
particular contrast of interest. These results are in an opposite direction in 
comparison with other Qdec analysis without covariates / ROI analysis on 
surface area residuals after removing effect of gender, age and right 
hemispheric surface area (Destrieux's labels) / Whole-brain VBM analyses with 
covariates (not on surface area then...)

Basically I have the feeling there is something wrong with the contrast display 
in this particular qdec analysis. I don’t know how I could get what I called 
the CSA residuals in the framework of this analysis.


2) Another question: should I standardize or center my covariates before 
proceeding to the analysis?


3) A silly question probably but to be 100% sure… If in the qdec.table.dat, 
order of subjects is first group “ dys “ then second group “ ct “ and that the 
contrast is called: rh-Diff-dys-dyslexic-control-intercept-area , negative p 
value means decrease of surface area in the first group (dys) as compared to 
the second group (ct), right ?


Thank you and best,
Damien MARIE





Douglas Greve 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+Greve%22>
 Wed, 28 Sep 2016 12:40:51 -0700 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20160928>

Those are not residuals. If you want residuals, you will need to run mri_glmfit 
from the command line adding --eres-save. You can get the command line from the 
mri_glmfit.log file in the glmdir





On 9/28/16 10:58 AM, Damien MARIE wrote:
Dear FreeSurfers,
Sorry for the repost. I’m still trying to extract the residuals of cortical 
surface area from a qdec analysis with two factors (2 levels) and 2 covariates.
I tried this command line:
mri_segstats --in 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh 
--sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf 
RH_Dys-CT_CSA_AgeGenderWRCSA.dat I’ve got a text file with 9 columns (number of 
clusters) and 69 lines (number of subjects). Now I am not 100% sure it’s really 
the residuals (y.mgh) so I would be glad if somebody could tell me please.
Best,
Damien
Original post:
Dear experts,

I would like to know what is the best and simplest way to extract cortical
surface area and thickness from clusters obtained after a Monte Carlo
correction. This is a group comparison I did with qdec including gender as
discrete variable + age and mean thickness or whole hemispheric surface area as
nuisance factors, so I would like to get the feature residuals after the
removal of the covariate effects.
I am sorry, I saw several posts about that but for me it’s not completely clear
what command line I should use to get tables for this…

Thank you and best,
Damien




*Damien MARIE*

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[Freesurfer] REPOST cluster feature extraction from qdec output

[Damien MARIE]

Dear FreeSurfers,

Sorry for the repost. I’m still trying to extract the residuals of cortical 
surface area from a qdec analysis with two factors (2 levels) and 2 covariates.

I tried this command line:

mri_segstats --in 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh 
--sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf 
RH_Dys-CT_CSA_AgeGenderWRCSA.dat

I’ve got a text file with 9 columns (number of clusters) and 69 lines (number 
of subjects).

Now I am not 100% sure it’s really the residuals (y.mgh) so I would be glad if 
somebody could tell me please.

Best,

Damien 





Original post:

Dear experts,

I would like to know what is the best and simplest way to extract cortical 
surface area and thickness from clusters obtained after a Monte Carlo 
correction. This is a group comparison I did with qdec including gender as 
discrete variable + age and mean thickness or whole hemispheric surface area as 
nuisance factors, so I would like to get the feature residuals after the 
removal of the covariate effects.
I am sorry, I saw several posts about that but for me it’s not completely clear 
what command line I should use to get tables for this… 

Thank you and best,
Damien




Damien MARIE
Post-doctoral Fellow
damien.ma...@unige.ch
+41 22 379 08 49
-
Brain and Language Lab
Department of Clinical Neuroscience
Biotech Campus
9 Chemin des Mines 1202 Genève
http://www.brainandlanguagelab.org
-


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[Freesurfer] cluster feature extraction from qdec output

[Damien MARIE]

Dear experts,

I would like to know what is the best and simplest way to extract cortical 
surface area and thickness from clusters obtained after a Monte Carlo 
correction. This is a group comparison I did with qdec including gender as 
discrete variable + age and mean thickness or whole hemispheric surface area as 
nuisance factors, so I would like to get the feature residuals after the 
removal of the covariate effects.

I am sorry, I saw several posts about that but for me it’s not completely clear 
what command line I should use to get tables for this… 

Thank you and best,
Damien
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[Freesurfer] Sulcal depth variations

[Damien MARIE]

Hello everyone,

I'm working on a group analysis of cortical thickness, surface area, curvature 
and sulcal depth with FreeSurfer 5.3. However I'm in trouble concerning the 
interpretation or the meaning of my results, especially concerning curvature 
and sulcal depth.

I understood that curvature can be positive when it concerns sulcus or positive 
in case of gyrus. According to my result it would be almost the same for sulcal 
depth. The value of sulcal depth is positive on a sulcus while it is negative 
on a gyrus.

Am I correct? 

All the best,

Damien Marie___
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