[Freesurfer] Quetion about thalamic nuclei segmentation in freesurfer v7

[Haewon Roh]

External Email - Use Caution

Hi. 

I have a quetion about thalamic nuclei segmentation process in freesurfer v7. 
Now, I’ve got  a large amounts of patients samples which were already 
pre-processed using “recon -all” pipeline in freesurfer version 6, but I want 
to know their specific volumes of thalamic nucleis or subsegmentations using 
freesufer 7.
 
So, due to a quite large number of samples, I feel that it will take a very 
long time to do preprocessing again in freesurfer 7 and , if possible, without 
re-pre-processing in freesurfer v7.0, I’d like to do additional subsegmentation 
of thalamus as well as hippoamygdala. 

So I’ like to ask if these kinds of thalmic nuclei subsegmentaion or 
Hippo-amygdala subsegmentation which was newly-introduced in freesurfer 7.0, 
can be done using data which was pre-processed in freesurfer 6.0 already.

(Is it possible to do thalamic segmentaiton using segmentThalamic nuclei 
pipeline in freesurfer 7 for the data already pre-processed in freesufer 6.0 ? 
) and I am also very curious if their results  will be different from the 
results which was made using only freesurfer v7 from pre-precessing?

Best, 
H Roh.

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Re: [Freesurfer] recon-all error

[Zollei, Lilla,Ph.D.]

Hi Nina,
The recon all pipeline uses an adult atlas. We have had collaborators 
successfully using it with subjects all the way down to age 4.5yrs, but under 
that it would not be recommended. Have you looked at the infant pipeline?
Best, Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wilpert, Nina- Maria 

Sent: Tuesday, August 4, 2020 10:51 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Schülke-Gerstenfeld, Markus 
Subject: [Freesurfer] mri: recon-all error


External Email - Use Caution

Hello FreeSurfer Developers,



We are attempting to run the command recon-all on pediatric MRI images (1-13 
yrs), as described on your website:

cmd=”recon-all -i $Dir/*.nii.gz -s sub02_test  -all”



The command worked well for some of our subjects. For others, however, hard 
failures occurred and recon-all did not finish or we received the following 
error (please find the recon-all.log attached):

“recon-all -s sub02_reconall exited with ERRORS at….”



Would you have any recommendations on how to trouble-shoot these issues? We 
have attached the recon-all.log documents in case it's of any use.



1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Linux

4) recon-all.log: see attached.



We would very much appreciate your help!



Kind regards,

Nina Wilpert







Nina-Maria Wilpert | medical student
T +49 (0) 30 450559858 | M +49 (0) 15783851445
E nina-maria.wilp...@charite.de

Department of Neuropediatrics

Charité, Universitätsmedizin Berlin

Institute of Anatomy

University of Leipzig

Genetics and Development of the Cerebral Cortex

Hôpital Necker-Enfants malades & IMAGINE, Paris




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Re: [Freesurfer] Help with LGI

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

External Email - Use Caution

Dear Freesurfer experts,

Just wanted to follow up my last email - does anyone know what might be
wrong with my code?

Thank you and stay safe,
Alex

On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental
Neuroscience, Lab of Autism and Developmental Neuroscience <
l...@email.gwu.edu> wrote:

> Dear Douglas,
>
> Yes, now matlab is correctly set to my freesurfer path, but the following
> error occurs when I run localGI (please see below). Any ideas what might be
> wrong? Maybe there are some issues with the matlab version or image
> processing toolbox that I'm using?
>
> iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4 -localGI
> Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> INFO: SUBJECTS_DIR is /Applications/BAP_complete
> Actual FREESURFER_HOME /Applications/freesurfer
> -rw-rw-r--  1 ajobsaid  982768932  956144 Jun 30 09:20
> /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log
> Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul  5
> 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
> /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms
> /Applications/BAP_complete/nih00024_epoch11_4
> /Applications/BAP_complete/nih00024_epoch11_4
> #@# white curv lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
>Update not needed
> #@# white area lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
>Update not needed
> #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
>Update not needed
> #@# pial area lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
>Update not needed
> #@# thickness lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> ../surf/lh.thickness
>Update not needed
> #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> ../surf/lh.thickness
>Update not needed
> #@# white curv rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
>Update not needed
> #@# white area rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
>Update not needed
> #@# pial curv rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
>Update not needed
> #@# pial area rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
>Update not needed
> #@# thickness rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> ../surf/rh.thickness
>Update not needed
> #@# area and vertex vol rh Fri Jul 31 09:20:05 PDT 2020
> cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> ../surf/rh.thickness
>Update not needed
> /Applications/BAP_complete/nih00024_epoch11_4/surf
> #
> #@# Local Gyrification Index lh Fri Jul 31 09:20:05 PDT 2020
> \n mris_compute_lgi --i lh.pial \n
> =
> rm -Rf
> /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial
> =
> =
> mkdir -p
> /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial
> =
> =
> mris_fill -c -r 1 lh.pial
> /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
> =
> reading surface from lh.pial...
> writing filled volume to
> /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
> conforming output volume
> setting resolution for intermediate calculations to 1.
> =
> make_outer_surface('/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
> exit
> =
>
>   

[Freesurfer] Converting surface files to ASCII - order of vertices

[Walsh, Shane W.]

Hi FreeSurfer community,

I have a set of .mgh patch files that are mapped to the FsAverage4 atlas. I'd 
like to do some calculations on the xyz coordinates of the vertices that make 
up a patch. I've been able to get ahold of these xyz coordinates by using 
mris_convert to convert FsAverage4 surface files to ASCII. I want to ensure the 
validity of these calculations, and in that process, I've run into two 
questions:

  1.  Do the order of vertices in a surface file match that of a 
mris_convert'ed ASCII surface file?
  2.  Do the order of vertices in the patches match that of the mris_convert'ed 
ASCII file?

In an attempt to answer to first question, I used Freeview to compare vertex 
coordinates in lh.inflated with lh.inflated.asc.

I'm able to use Freeview to visualize the surface files and click on any vertex 
to get its xyz coordinates. However, the set of coordinates given in Freeview 
seems to be completely different than the set of coordinates given in the ASCII 
version of the surface file.

I think this issue is best demonstrated by an example. If I load 
subjects/fsaverage4/surf/lh.inflated into Freeview, the first vertex (Vertex 0) 
is listed at [-36.79, -18.60, 64.82]. Not only is this coordinate different 
from the one on the first line of lh.inflated.asc, it's not contained anywhere 
in the file.

I looked into if the the coordinates differ by a constant if we assume that 
they're listed in the same order in both files, but I found this not to be the 
case.

Based on this information, I'm unsure of the answer to my first question. My 
suspicion is that there is some sort of transform applied to the coordinates. I 
feel like I would need to figure out the first question before I can answer the 
second.

I've hit a dead end and any guidance on either question would be greatly 
appreciated.

Thank you,
Shane Walsh
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[Freesurfer] Change in volume driven by SA or CT?

[Meike Hettwer]

External Email - Use Caution

Dear Freesurfer Experts

I am trying to get more information about a cluster indicating a change 
in cortical volume as a function of a continuous variable. I am 
currently considering different approaches to find out if this change in 
volume is primarily explained by a change in surface area or cortical 
thickness. Is there a standard procedure that freesurfer users go for to 
do this? (Otherwise I would probably extract volume, SA and CT values 
from the cluster and run an external analysis.)

Thanks a lot,

Doro




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[Freesurfer] Fwd: using own skull stripped t1

[Julie Ottoy]

External Email - Use Caution

Hi Freesurfer team

I was wondering if you’d have some time to take a look at question below.
Thanks!

-- Forwarded message -
From: Julie Ottoy 
Date: Thu, 30 Jul 2020 at 13:22
Subject: using own skull stripped t1
To: Freesurfer support list 


Dear freesurfer team

I'm trying to use my own skull stripped T1 when running recon-all. For
this, I'm doing following steps:
1) run recon-all with -autorecon-1 -noskullstrip
2) mri_convert --in_type nii --out_type mgz -rl
./FreeSurfer/ID/mri/orig.mgz -rt nearest ./own_skull_strip.nii.gz
./FreeSurfer/ID/mri/brainmask.mgz
3) run recon-all with -autorecon-2 and autorecon-3

My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore,
when transforming to the size of brainmask.mgz (256x256x256), it deforms. I
tried nearest, cubic, and interpolate, but none of them gives actually a
good result in terms of retaining the contrast. I was wondering if it is
important to keep a good contrast for brainmask.mgz , or whether this
brainmask.mgz is just used to determine the brain borders for segmentation.
(ie.: in which steps of recon-all is the brainmask.mgz actually used?)

Any recommendations?

Thank you!
Julie
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Re: [Freesurfer] How to do permutation for multiple comparison correction?

[Xiaojiang Yang]

External Email - Use Caution

Thank you! Now I see how permutation works. So given about 100-200 subjects
in the normal group, doing 1000 permutations is of no help.

In fact, in my cortical thickness abnormality test, no matter how many
times of permutations I take, the original non-permutated data is the only
one arrangement I can observe that has a "big" cluster area - all
permutated data has no cluster of big continuous area (given the
vertex-wise threshold). So, permutations cannot give me a reasonable
probabulity distribution of the sampling data, which means I cannot rely
on it to reduce False Positives. Very frustrated here. If you have more
comments here, please let me know. Thanks.

Best Regards,
Xiao


Douglas N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22>
 Tue, 04 Aug 2020 08:27:47 -0700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200804>

There are actually only N-1 permutations that you can make:

Real matrix:
1 0
0 1
0 1
0 1
0 1


Permutation 1:

0 1
1 0
0 1
0 1
0 1


Permutation 2:

0 1
0 1
1 0
0 1
0 1




On 8/4/2020 10:41 AM, Xiaojiang Yang wrote:

External Email - Use Caution

Hi Doug,


I am still uncertain how to permutate the data for multiple comparisons.
Please help me with a little more details on this. For example, could you
give me 2-3 examples of the permutations for the matrix you gave to me?

In addition, if you can explain to me in a non-design-matrix way, that would
be great. For example, suppose I have 1 subject to be compared to n
subjects in a normal group. The number of comparisons is m. So I have m x
(1+n) data in total:

V_10   V_11 , V_12 , V_13 , … V_1n

V_20   V_21 , V_22 , V_23 , … V_2n

…… …… …… ……

V_m0  V_m1 , V_m2 , V_m3 , … V_mn

_


_Could you please explain to me how data should be permutated? Or give me
2-3 examples of the permutations of the above data that could be?

_Thank you a lot!

Xiao


Douglas N. Greve <
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22
>Thu, 23 Jul 2020 10:54:17 -0700 <
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200723
>

You would have a design matrix with two columns and rows equal to n+1, eg
1  0
0 1
0 1
0 1
0 1
... n times
you would then permute the design matrix

On 7/23/2020 12:06 PM, Xiaojiang Yang wrote:

 External Email - Use Caution

Hi Doug,

For the first question, you answered "It is unusual, though it
should work". Could you please briefly describe the way FS used to
permute (based on my notation v0, v1, ... vn)? Or, the usual way
to permute?The way I described seems to be the only way I can
think of. Looking forward to your help here. Thanks a lot!

Xiao

Douglas N. Greve

<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22>Thu,
23 Jul 2020 07:37:13 -0700

<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200723>


On 7/21/2020 11:45 AM, Xiaojiang Yang wrote:

  External Email - Use Caution

 Hi Doug,
 For your questions:

 1. "Not sure what you mean by in the ROI. Are you trying to
 permute across space? That generally does not work because the
 points are not exchangeable across space."

 By "In the ROI", I mean for all vertices listed in the label file.
Here, I
am
 talking about a test subject and n control subjects, they are all
considered in the same
 reference subject space - fsaverage. A ROI is defined by a label file
for
the subject
 fsaverage. So, I am comparing the test subject and control group on the
same ROI region,
 vertex by vertex. I want to permute points in the test subject and
points
in all subjects
 in control groups.
 I am not talking about permuting vertex locations; I am talking about
permuting
 values (thickness in my case) from subjects on each vertex. For
example, for
 vertex i, I have one value (v0) from test subject, and n values (v1,
v2,...vn)
 from control subjects:
 test subject  control subjects
 v0v1, v2, .. vn
 One way of permutation would be:
 test subject  control subjects
 v1v0, v2, .. vn
 Is this a reasonable way to do permutation?

It is unusual, though it should work.

 2. "Not sure. You cannot discriminate between the groups when you
 are doing permutation"

 By doing the permutation many (say 1000) times, I want to get the
probability
 distribution of the sampling 

Re: [Freesurfer] How to do permutation for multiple comparison correction?

[Douglas N. Greve]

There are actually only N-1 permutations that you can make:

Real matrix:
1 0
0 1
0 1
0 1
0 1


Permutation 1:

0 1
1 0
0 1
0 1
0 1


Permutation 2:

0 1
0 1
1 0
0 1
0 1




On 8/4/2020 10:41 AM, Xiaojiang Yang wrote:


External Email - Use Caution

Hi Doug,

I am still uncertain how to permutate the data for multiple 
comparisons. Please help me with a little more details on this. For 
example, could you give me 2-3 examples of the permutations for the 
matrix you gave to me?


In addition, if you can explain to me in a non-design-matrix way, that 
would be great. For example, suppose I have 1 subject to be compared 
to n subjects in a normal group. The number of comparisons is m. So I 
have m x (1+n) data in total:


V_10   V_11 , V_12 , V_13 , … V_1n

V_20   V_21 , V_22 , V_23 , … V_2n

…… …… …… ……

V_m0  V_m1 , V_m2 , V_m3 , … V_mn

_

_Could you please explain to me how data should be permutated? Or give 
me 2-3 examples of the permutations of the above data that could be?


_Thank you a lot!

Xiao

Douglas N. Greve 
Thu, 
23 Jul 2020 10:54:17 -0700 


You would have a design matrix with two columns and rows equal to n+1, eg
1  0
0 1
0 1
0 1
0 1
... n times
you would then permute the design matrix

On 7/23/2020 12:06 PM, Xiaojiang Yang wrote:

 External Email - Use Caution

Hi Doug,

For the first question, you answered "It is unusual, though it
should work". Could you please briefly describe the way FS used to
permute (based on my notation v0, v1, ... vn)? Or, the usual way
to permute?The way I described seems to be the only way I can
think of. Looking forward to your help here. Thanks a lot!

Xiao

Douglas N. Greve

Thu,
23 Jul 2020 07:37:13 -0700




On 7/21/2020 11:45 AM, Xiaojiang Yang wrote:

  External Email - Use Caution

 Hi Doug,
 For your questions:

 1. "Not sure what you mean by in the ROI. Are you trying to
 permute across space? That generally does not work because the
 points are not exchangeable across space."

 By "In the ROI", I mean for all vertices listed in the label file. 
Here, I
am
 talking about a test subject and n control subjects, they are all
considered in the same
 reference subject space - fsaverage. A ROI is defined by a label file 
for
the subject
 fsaverage. So, I am comparing the test subject and control group on the
same ROI region,
 vertex by vertex. I want to permute points in the test subject and 
points
in all subjects
 in control groups.
 I am not talking about permuting vertex locations; I am talking about
permuting
 values (thickness in my case) from subjects on each vertex. For 
example, for
 vertex i, I have one value (v0) from test subject, and n values (v1,
v2,...vn)
 from control subjects:
 test subject  control subjects
 v0v1, v2, .. vn
 One way of permutation would be:
 test subject  control subjects
 v1v0, v2, .. vn
 Is this a reasonable way to do permutation?

It is unusual, though it should work.

 2. "Not sure. You cannot discriminate between the groups when you
 are doing permutation"

 By doing the permutation many (say 1000) times, I want to get the
probability
 distribution of the sampling (observed or test) data inside the ROI 
area, so
 that I can decide if I should reject or accept null hypothesis based on
 cluster-wise significance level. What problems do you think I have in 
this
idea?

That should work. I'm not sure what my original concern was

 Thanks a lot!
 On 7/21/2020 1:12 AM, Xiaojiang Yang wrote:

   External Email - Use Caution

  Dear FS experts,

  Instead of using mri_glmfit-sim, I am trying to implement a
  customized multiple comparison correction algorithm using
  permutation. Before I implement my own, I want to make sure my
  permutation idea is correct. So I was looking at how
  mri_glmfit-sim does the permutation. The link here
  http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm has     

Re: [Freesurfer] peak MNI coordinates within a masked sig.mgh

[Fred Sampedro]

External Email - Use Caution

Thanks a lot!

I read the mri_volcluster doc, can you confirm that the TalX TalY TalZ
coordinates are those of the vertex with maximum intensity within the
cluster? (it could be those of the cluster's center of gravity)

Finally, I would be very grateful if you could help me with minor parameter
tuning of the commands:



1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG?(how do I get it?)
--o roimask.mgh

2) fslcalc sig.mgh mult roimask.mgh -o maskedsig.mgh

3) mri_volcluster --in maskedsig.mgh --thmin 0.001 --sum output.txt





Thanks a lot in advance!

On Mon, Aug 3, 2020 at 4:40 PM Douglas N. Greve 
wrote:

> Try mri_volcluster. Pass you masked sig as the input and set --thmin
> 0.0001 and specify a summary file with --sum. I think that should work
>
> On 7/31/2020 9:38 AM, Fred Sampedro wrote:
>
> External Email - Use Caution
> Dear FS experts,
>
> I have a rather simple question:
>
> I would like to obtain the MNI coordinates of the most significant vertex
> in a sig.mgh map but within a specific ROI (for instance the left
> supramarginal region).
>
> Here is my attempt but with practical gaps in terms of command parameters:
>
> 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG? --o roimask.mgh
>
> 2) fslmaths sig.mgh mult roimask.mgh -o maskedsig.mgh
>
> 3) which command could I use to obtain the MNI coordinates of the peak
> value in maskedsig.mgh?
>
> Thanks a lot in advance!
>
> ___
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>
>
> ___
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Re: [Freesurfer] How to do permutation for multiple comparison correction?

[Xiaojiang Yang]

External Email - Use Caution

Hi Doug,

I am still uncertain how to permutate the data for multiple comparisons.
Please help me with a little more details on this. For example, could you
give me 2-3 examples of the permutations for the matrix you gave to me?

In addition, if you can explain to me in a non-design-matrix way, that
would be great. For example, suppose I have 1 subject to be compared to n
subjects in a normal group. The number of comparisons is m. So I have m x
(1+n) data in total:

V10  V11, V12, V13, … V1n

V20  V21, V22, V23, … V2n

…… …… …… ……

Vm0 Vm1, Vm2, Vm3, … Vmn


Could you please explain to me how data should be permutated? Or give me
2-3 examples of the permutations of the above data that could be?

Thank you a lot!
Xiao

Douglas N. Greve

 Thu, 23 Jul 2020 10:54:17 -0700


You would have a design matrix with two columns and rows equal to n+1, eg
1  0
0 1
0 1
0 1
0 1
... n times

you would then permute the design matrix

On 7/23/2020 12:06 PM, Xiaojiang Yang wrote:

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Hi Doug,


For the first question, you answered "It is unusual, though it should work".
Could you please briefly describe the way FS used to permute (based on my
notation v0, v1, ... vn)? Or, the usual way to permute?

The way I described seems to be the only way I can think of. Looking
forward to your help
here. Thanks a lot!

Xiao


Douglas N. Greve <
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22
>Thu, 23 Jul 2020 07:37:13 -0700 <
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200723
>

On 7/21/2020 11:45 AM, Xiaojiang Yang wrote:

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Hi Doug,
For your questions:

1. "Not sure what you mean by in the ROI. Are you trying to
permute across space? That generally does not work because the
points are not exchangeable across space."

By "In the ROI", I mean for all vertices listed in the label file. Here, I
am
talking about a test subject and n control subjects, they are all
considered in the same
reference subject space - fsaverage. A ROI is defined by a label file for
the subject
fsaverage. So, I am comparing the test subject and control group on the
same ROI region,
vertex by vertex. I want to permute points in the test subject and points
in all subjects
in control groups.
I am not talking about permuting vertex locations; I am talking about
permuting
values (thickness in my case) from subjects on each vertex. For example, for
vertex i, I have one value (v0) from test subject, and n values (v1,
v2,...vn)
from control subjects:
test subject  control subjects
v0v1, v2, .. vn
One way of permutation would be:
test subject  control subjects
v1v0, v2, .. vn
Is this a reasonable way to do permutation?

It is unusual, though it should work.

2. "Not sure. You cannot discriminate between the groups when you
are doing permutation"

By doing the permutation many (say 1000) times, I want to get the
probability
distribution of the sampling (observed or test) data inside the ROI area, so
that I can decide if I should reject or accept null hypothesis based on
cluster-wise significance level. What problems do you think I have in this
idea?

That should work. I'm not sure what my original concern was

Thanks a lot!
On 7/21/2020 1:12 AM, Xiaojiang Yang wrote:

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 Dear FS experts,

 Instead of using mri_glmfit-sim, I am trying to implement a
 customized multiple comparison correction algorithm using
 permutation. Before I implement my own, I want to make sure my
 permutation idea is correct. So I was looking at how
 mri_glmfit-sim does the permutation. The link here
 http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
has


<
http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm%C2%A0has
>

 a simple description for how to do permutation, but I don't quite
 understand the 1st step: Permute the design matrix. To me, permute
 the design matrix means permute the matrix rows here, but still
 hard to understand why permuting matrix rows does the trick.

This is pretty standard in permutation. I think Tom Nichols has
some basic tutorials on how permutations work.

 Anyway, I will not use any design matrix in my customized
 implementation, so it does not matter 

Re: [Freesurfer] Change in volume driven by SA or CT?

[Douglas N. Greve]

I would probably just extract the values. Anderson Winkler wrote a paper 
on this a few years ago, so you might want to look that up.


On 8/4/2020 10:03 AM, Meike Hettwer wrote:
>  External Email - Use Caution
>
> Dear Freesurfer Experts
>
> I am trying to get more information about a cluster indicating a change
> in cortical volume as a function of a continuous variable. I am
> currently considering different approaches to find out if this change in
> volume is primarily explained by a change in surface area or cortical
> thickness. Is there a standard procedure that freesurfer users go for to
> do this? (Otherwise I would probably extract volume, SA and CT values
> from the cluster and run an external analysis.)
>
> Thanks a lot,
>
> Doro
>
>
>
>
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Re: [Freesurfer] Recon-all Soft Errors

[Douglas N. Greve]

Can you send a picture of the type of errors you are seeing?

On 7/31/2020 9:03 AM, Elana Sarabin wrote:

 External Email - Use Caution

Here is the recon-all.log file.

Thanks,
Elana

-Original Message-
From: Elana Sarabin
Sent: July 30, 2020 10:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: Recon-all Soft Errors

Here is the recon-all.log file.

Thanks,
Elana

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of 
freesurfer-requ...@nmr.mgh.harvard.edu
Sent: July 30, 2020 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 197, Issue 59

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Contents of Freesurfer digest..."


Today's Topics:

1. FS 7.1.0 - Editing intensity values for WM (Nils B?er)
2. Re: FS 7.1.0 - Editing intensity values for WM (Fischl, Bruce)
3. Creating .annot file for a mri_decimate downsampeld   version
   of pial surface (Donelson Berger)
4. GONE: -make to recon-all (Johnson, Hans J)
5. Re: fsgd file - glmfit error
   (Lab of Autism and Developmental Neuroscience,Lab of Autism and 
Developmental Neuroscience)
6. Re: Recon-all Soft Errors (Zollei, Lilla,Ph.D.)
7. bad interpreter: No such file or directory error
   (Hengameh Marzbani)
8. Re: overlapping/ superimposing regions of one analysis over
   another (Douglas N. Greve)
9. Re: Creating .annot file for a mri_decimate downsampeld
   version of pial surface (Douglas N. Greve)
   10. Re: Recon-all Soft Errors (Douglas N. Greve)
   11. Re: Coregistration to MNI (Douglas N. Greve)
   12. mri_aparc2aseg: how to remove redundant output labels? (Ellen Ji)
   13. Re: bad interpreter: No such file or directory error (fsbuild)


--

Message: 1
Date: Wed, 29 Jul 2020 21:27:03 +0200
From: Nils B?er 
Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
 
Content-Type: text/plain; charset="utf-8"

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Hello everyone,

I just have a short question, because I can't find anything helpful in the 
tutorials.

In my MRI scans freesurfer includes areas to the white matter, even though 
visual inspection concludes that the area should be grey matter. Is there a 
possibility to change the value at which freesurfer includes areas to the WM, 
which i can just change? For example freesurfer includes areas to the WM with 
intensity values below 85 and i want to change that.

I'd be thankful for any feedback/links to guides.

Best regards,

Nils
--

Nils B?er
Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* 
University of Paderborn Department of Sports and Health Warburger Str. 100
33098 Paderborn
Room: Sp 1.401

Email: nils.tobia...@gmail.com / nbo...@mail.uni-paderborn.de 

Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/
  https://sug.uni-paderborn.de/department/it/



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Message: 2
Date: Wed, 29 Jul 2020 20:32:34 +
From: "Fischl, Bruce" 
Subject: Re: [Freesurfer] FS 7.1.0 - Editing intensity values for WM
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID:
 


Content-Type: text/plain; charset="utf-8"

Hi Nils

There are expert options for this. You can specify things like -min_white 90 to 
some of the programs like mri_segment and the surface placement stuff

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nils B?er
Sent: Wednesday, July 29, 2020 3:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM


 External Email - Use Caution
Hello everyone,

I just have a short question, because I can't find anything helpful in the 
tutorials.

In my MRI scans freesurfer includes areas to the white matter, even though 
visual inspection concludes that the area should be grey matter. Is there a 
possibility to change the value at 

Re: [Freesurfer] Recon-all error when refining pial surfaces with T2 FLAIR

[Douglas N. Greve]

Can you send the subject to us? See below for instructions

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.



On 8/1/2020 12:08 AM, Pankush Kumar wrote:


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Hello,

I am a student using freesurfer 7.1.0 having some trouble with 
recon-all on some subjects. I am trying to calculate pial surfaces by 
adding FLAIR images to my T1 (already processed on recon-all 
beforehand), but encounter the following error:


Starting loop over 121584 vertices
   vno = 0, t = 1.21632
   vno = 2, t = 3.38757
   vno = 4, t = 8.77043
   vno = 6, t = 11.8685
   vno = 8, t = 14.6273
error: Numerical result out of range
error: MRIhistogramLabelRegion: constant image

Log is attached. Other subjects get stuck on the vno = 8 step and 
run for days without progress. No artifacts in any of the images, but 
some have obvious structural variation such as enlarged and misshapen 
ventricles.


Thank you, any help would be greatly appreciated!

Sincerely,
Pankush Kumar

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