Re: [Freesurfer] Version 6.0 patches for hi-res data

[Alexopoulos, Dimitrios]

External Email - Use Caution

Ok. But the updated patches will need to be applied to the data generated with 
the -hires flag?

Jim


On Jan 24, 2020 5:32 PM, "Greve, Douglas N.,Ph.D."  
wrote:
For the -conf2hires, there is no problem because the segmentation is done at 
1mm.

On 1/24/2020 5:17 PM, Alexopoulos, Dimitrios wrote:

External Email - Use Caution

I came across info for version 6.0 that generated statistical errors when using 
high resolution input.

https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed



We have used the ‘-hires’ flag and, more recently, the ‘-conf2hires’ flag with 
recon-all.v6.hires command. Our input data is 0.8mm^3

I presume we only need to rerun the stats using the mri_segstats and 
mris_anatomical_stats patches, correct?



Jim











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Re: [Freesurfer] Version 6.0 patches for hi-res data

[Greve, Douglas N.,Ph.D.]

For the -conf2hires, there is no problem because the segmentation is done at 
1mm.

On 1/24/2020 5:17 PM, Alexopoulos, Dimitrios wrote:

External Email - Use Caution
I came across info for version 6.0 that generated statistical errors when using 
high resolution input.
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed

We have used the ‘-hires’ flag and, more recently, the ‘-conf2hires’ flag with 
recon-all.v6.hires command. Our input data is 0.8mm^3
I presume we only need to rerun the stats using the mri_segstats and 
mris_anatomical_stats patches, correct?

Jim





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



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[Freesurfer] Version 6.0 patches for hi-res data

[Alexopoulos, Dimitrios]

External Email - Use Caution

I came across info for version 6.0 that generated statistical errors when using 
high resolution input.
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed

We have used the '-hires' flag and, more recently, the '-conf2hires' flag with 
recon-all.v6.hires command. Our input data is 0.8mm^3
I presume we only need to rerun the stats using the mri_segstats and 
mris_anatomical_stats patches, correct?

Jim





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
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Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

[Iglesias Gonzalez, Juan E.]

Good question! It’s ok if only the hippo is covered.
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Rene Seiger 

Reply-To: Freesurfer support list 
Date: Friday, 24 January 2020 at 12:15
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool 
(incl Amygdala) FreeSurfer_dev version


External Email - Use Caution

Dear Juan,

Thank you very much for you answer! However, I ran into another issue using the 
new tool: It is stated:  'Using the additional scan in isolation is advised 
when it is of higher resolution than the T1 while covering the whole hippocampi 
and amygdalae'. Can I still use this processing mode, when my high-resolution 
scans only have the hippocampi covered, as I am not interested in the amygdala 
in the first place? Or is it mandatory to have both structures fully covered 
within the additional scan when I want to run it in isolation?
Thank you very much,
René





Am 23.01.2020 um 18:09 schrieb Iglesias Gonzalez, Juan E.:
Hi Rene,
The atlases are slightly different so the outputs will be a bit different. But 
the segmentations will indeed be comparable.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From: 

 on behalf of Rene Seiger 

Reply-To: Freesurfer support list 

Date: Thursday, 23 January 2020 at 07:48
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl 
Amygdala) FreeSurfer_dev version


External Email - Use Caution

Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems to be 
obsolete and it looks as if this module will be replaced by a newer version in 
the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).

However, I am not entirely sure how those two modules differ in terms of 
hippocampal subfield segmentation, when the "FS60" parcellation scheme is used 
in the new module. It is stated that 'it mimics the FreeSurfer 6.0 hippocampal 
module', but is the output 1:1 comparable?
Thank you very much and kind regards,
René
--

Dr. René Seiger
Research Associate

Medical University of Vienna
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
http://www.meduniwien.ac.at/neuroimaging/





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Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

[Rene Seiger]

   External Email - Use Caution


Dear Juan,

Thank you very much for you answer! However, I ran into another issue 
using the new tool: It is stated:  'Using the additional scan in 
isolation is advised when it is of higher resolution than the T1 while 
covering the whole hippocampi and amygdalae'. Can I still use this 
processing mode, when my high-resolution scans only have the hippocampi 
covered, as I am not interested in the amygdala in the first place? Or 
is it mandatory to have both structures fully covered within the 
additional scan when I want to run it in isolation?


Thank you very much,
René





Am 23.01.2020 um 18:09 schrieb Iglesias Gonzalez, Juan E.:


Hi Rene,

The atlases are slightly different so the outputs will be a bit 
different. But the segmentations will indeed be comparable.


Cheers,

/Eugenio

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: * on behalf of Rene 
Seiger 

*Reply-To: *Freesurfer support list 
*Date: *Thursday, 23 January 2020 at 07:48
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *[Freesurfer] Hippocampal subfields FS6 vs. new hippocampus 
tool (incl Amygdala) FreeSurfer_dev version


*External Email - Use Caution *

Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems 
to be obsolete and it looks as if this module will be replaced by a 
newer version in the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).


However, I am not entirely sure how those two modules differ in terms 
of hippocampal subfield segmentation, when the "FS60" parcellation 
scheme is used in the new module. It is stated that 'it mimics the 
FreeSurfer 6.0 hippocampal module', but is the output 1:1 comparable?


Thank you very much and kind regards,
René

--

*Dr. René Seiger*
Research Associate

*Medical University of Vienna*
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
http://www.meduniwien.ac.at/neuroimaging/ 






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Re: [Freesurfer] freesurfer container - freeview error

[Hoopes, Andrew]

Unfortunately, I'm not sure if that original dockerfile is available anymore, 
but freeview was never intended to be run from that image anyway as X11 
forwarding wasn't supported (maybe it is now though). I'd recommend following 
marcosm's suggestion of tackling the library errors as they appear. Installing 
xorg and mesa-libGLU should be a good place to start.

best
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Arnaud Boré 

Sent: Friday, January 17, 2020 3:16 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer container - freeview error

External Email - Use Caution

Hi,

Thank you for your quick response. Is there a way to have access to the 
definition of the official docker? I could also help to find which libraries 
are missing.

Thank you for help
Arnaud

Le ven. 17 janv. 2020 12 h 00, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> a écrit :
Hi Arnaud,

If you want to forward graphics from singularity, you will probably need to 
install some extra libraries in the container. I've never actually tested this, 
so I'm not even sure that it's possible, but according to singularity's doc at 
https://singularity-tutorial.github.io you should at least try to install xorg 
and work from there.

best
Andrew


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Arnaud Boré mailto:arnaud.b...@gmail.com>>
Sent: Friday, January 17, 2020 11:34 AM
To: Freesurfer support list
Subject: [Freesurfer] freesurfer container - freeview error

External Email - Use Caution

Dear Freesurfer' experts,

I've created a singularity container from the official docker hub freesurfer 
repository (https://hub.docker.com/r/freesurfer/freesurfer)

When running: singularity exec freesurfer.sif freeview I get this error:

freeview_bin: error while loading shared libraries: libGLU.so.1: cannot open 
shared object file: No suche file or directory.

I would like to know if this is something related to the containers or the host 
computer and some tips to fix this. I tested the singularity on different 
computers/laptops and ended up with the same error so I think there is an issue 
with the singularity/docker container.

Thank you in advance
Arnaud

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Re: [Freesurfer] FreeSurfer analyses in MatLab

[Graduate Imaging]

External Email - Use Caution

On Fri, Jan 24, 2020 at 10:32 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

>
>
> On 1/22/2020 2:13 PM, Graduate Imaging wrote:
>
> External Email - Use Caution
>
>
> On Tue, Jan 21, 2020 at 10:40 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>>
>>
>> On 1/17/2020 10:39 AM, Graduate Imaging wrote:
>>
>> External Email - Use Caution
>>
>>> Hello,
>>>
>>> I recently ran a vertex wise analysis on two different projects the
>>> first had three groups with three co-variates that looked at if group
>>> membership was associated with brain volume. The second project had two
>>> groups with three co-variates looking at psychiatric x BMI interaction
>>> effect on brain volume. I'm interested in running ROI analyses in matlab to
>>> ensure the same matrices were used.
>>>
>>> To run the ROI analyses I'm going to important the design matrix from
>>> the vertex wise analysis and use the fast_glmfit and fast_fratio commands
>>> as shown below:
>>> X = load('Xg.dat');
>>> C = load('C.dat');
>>> y = load('ROI.dat'); text file containing participant ROI values from
>>> the DKT atlas.
>>> [beta rvar] = fast_glmfit(y,X);
>>> [F pvalues] = fast_fratio(beta,X,rvar,C
>>>
>>> My first question is the beta values that are calculated from
>>> fast_glmfit are unstandardized is there anyway way to have it compute
>>> standardized values?
>>>
>>> I think this is how you would compute that
>>> betastddev = sqrt(rvar*diag(inv(X'*X)));
>>> betastandard = beta./betastddev;
>>>
>> When I try running this in Matlab I get the Error using  ***  incorrect
>> dimensions for matrix multiplication message.
>>
>> That means that the number of items in y (ie, number of subjects in
>> ROI.dat) is different than the number of rows in X (number of subjects in
>> the fsgd). What are the sizes of y and X?
>>
> That's what I suspected as well however, X = 102x12 and Y= 102x5. I ran
> [betastddev = sqrt(rvar*diag(inv(X'*X))); betastandard = beta./betastddev]
> after running successfully running [[beta rvar] = fast_glmfit(Y,X); [F
> pvalues] = fast_fratio(beta,X,rvar,C)] so its odd that the the dimensions
> wouldn't be matching.
>
> Also when using fast_glmfit and fast_fratio via Matlab for ROI analyses
> what are the appropriate papers to cite? In the Matlab files in fsfast
> there is reference to Worsley, K.J. and Friston, K.J. Analysis of fMRI
> Time-Series Revisited - Again. Neuroimage 2, 173-181, 1995. Would this be
> the correct citation?
>
> The GLM is so old I would not know what to cite. If you feel you need to
> cite something, that Worsley paper is fine.
>
Thanks. For DODS looking at an interaction term for the previously
mentioned 2 group 4 co-variate analysis it produces the beta weights for
each of the 10 regressors. Am I correct is assuming the way the analysis
works is that it creates interaction terms for the class with each of the
co-variates? If so the analysis could be summarized by Y = B0 + B1*X1 +
B2*X2 + B3*X3 + B4X4 + B5X5 + B6*X1*X2 + B7*X1*X3 + B8*X1*X4 + B9*X1*X5 +
e. Where X1= Class, X2= BMI, X3=ICV, X4= Age and X5=sex (I've since
incorporated this to be apart of class but want to continue with this
example). If that is the case to get an overall interaction term I should
be able to manually create these interaction terms and put them into a
matrix then for the contrast just regress out all of the effects except for
the BMI*class (B6*X1*X2). However, when I do this the p value is not the
same (far more significant) than using the DODS analysis with the 0 0 1 -1
0 0... contrast.




>
>>> My second question is when I ran the ROI analyses looking at the
>>> diagnosis x BMI interaction effect it outputs an array of beta values for
>>> each regressor. In addition to each groups beta value (for BMI) I'm
>>> interested in the beta value of the interaction (ie diagnosis x BMI). I was
>>> wondering how do i go about obtaining this? Would I have to create a new
>>> matrix with the interaction term included in it?
>>>
>>> If so would the analysis essentially be one group with the diagnosis x
>>> BMI interaction term plus the three co-variates?
>>>
>>> If you are using an FSGD file and have used DODS, then you can create an
>>> interaction contrast. Send me your fsgd file if you want further help
>>>
>> Yes I was using DODS approach for this analysis, I've attached my FSGD
>> file to this email.
>>
>>
>> You have 2 groups and 4 coviariates so 10 regressors. The dx BMI
>> interaction would need a contrast matrix
>> 0 0 1 -1 0 0 ... the rest 0s
>> BTW, sex should not be a covariate. You really need to have four groups,
>> P-male, P-female, HC-male, and HC-female (which would change the contrast
>> above)
>> Also, I would normalize the age and ICV
>>
>> Thanks for the correction I'll update my matrix accordingly to four
> groups and normalize the variables! The contrast matrix I ran was actually
> the same you suggested however it pastes an array 

Re: [Freesurfer] help: fs-fast group level analysis per run

[Greve, Douglas N.,Ph.D.]

The run-wise functionality was added after selxavg was written as a way to help 
debug. If you want all the runs in your group analysis, why not turn off the 
run-wise flag?

On 1/22/2020 4:40 PM, Rami Hamati wrote:

External Email - Use Caution

Hello freesurfers,

I'm attempting to run second-level analysis on separate runs of a brain scan, 
that were generated by selxavg3-sess -run-wise (pr001, pr002, pr003, pr004) as 
described in selxavg3-sess --help.

But, when attempting to concatenate the data using isxconcat-sess, (as 
described here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel ) 
there is no similar -run-wise function. I've searched the list and no similar 
errors have been reported.. I am wondering if there is a command or workaround 
for this. Thank you very much!

--
Rami Hamati, MSc.
Royal's Institute of Mental Health Research
Molecular Imaging Laboratory (MIL)
1145 Carling Ave, Ottawa, ON K1Z 7K4

rami.ham...@theroyal.ca
rhama...@uottawa.ca




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Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

[Greve, Douglas N.,Ph.D.]

It did not look like there was an explicit error in that log file, it just 
stops at mris_volmask. Is that the right recon-all? Also, please just send the 
text file so that we don't have to unzip it.

On 1/22/2020 4:39 PM, Laurel Quinlan wrote:

External Email - Use Caution

Hi FS Support,

I have two brains for which recon-all exited with errors after I edited the 
wm.mgz volume. It seems that the problem occurs during the mri_segstats and 
mri_relabel_hypointensities steps (if I'm reading the output of the command 
"tail scripts/recon-all.log" correctly). I attached one of the recon-all.log 
files as a zipped txt file. Please let me know if you have troubleshooting 
suggestions.

Thank you for your help!

Laurel Quinlan
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison




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Re: [Freesurfer] FreeSurfer analyses in MatLab

[Greve, Douglas N.,Ph.D.]

On 1/22/2020 2:13 PM, Graduate Imaging wrote:

External Email - Use Caution


On Tue, Jan 21, 2020 at 10:40 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:


On 1/17/2020 10:39 AM, Graduate Imaging wrote:

External Email - Use Caution

Hello,

I recently ran a vertex wise analysis on two different projects the first had 
three groups with three co-variates that looked at if group membership was 
associated with brain volume. The second project had two groups with three 
co-variates looking at psychiatric x BMI interaction effect on brain volume. 
I'm interested in running ROI analyses in matlab to ensure the same matrices 
were used.

To run the ROI analyses I'm going to important the design matrix from the 
vertex wise analysis and use the fast_glmfit and fast_fratio commands as shown 
below:
X = load('Xg.dat');
C = load('C.dat');
y = load('ROI.dat'); text file containing participant ROI values from the DKT 
atlas.
[beta rvar] = fast_glmfit(y,X);
[F pvalues] = fast_fratio(beta,X,rvar,C

My first question is the beta values that are calculated from fast_glmfit are 
unstandardized is there anyway way to have it compute standardized values?
I think this is how you would compute that
betastddev = sqrt(rvar*diag(inv(X'*X)));
betastandard = beta./betastddev;
When I try running this in Matlab I get the Error using  *  incorrect 
dimensions for matrix multiplication message.
That means that the number of items in y (ie, number of subjects in ROI.dat) is 
different than the number of rows in X (number of subjects in the fsgd). What 
are the sizes of y and X?
That's what I suspected as well however, X = 102x12 and Y= 102x5. I ran 
[betastddev = sqrt(rvar*diag(inv(X'*X))); betastandard = beta./betastddev] 
after running successfully running [[beta rvar] = fast_glmfit(Y,X); [F pvalues] 
= fast_fratio(beta,X,rvar,C)] so its odd that the the dimensions wouldn't be 
matching.

Also when using fast_glmfit and fast_fratio via Matlab for ROI analyses what 
are the appropriate papers to cite? In the Matlab files in fsfast there is 
reference to Worsley, K.J. and Friston, K.J. Analysis of fMRI Time-Series 
Revisited - Again. Neuroimage 2, 173-181, 1995. Would this be the correct 
citation?
The GLM is so old I would not know what to cite. If you feel you need to cite 
something, that Worsley paper is fine.

My second question is when I ran the ROI analyses looking at the diagnosis x 
BMI interaction effect it outputs an array of beta values for each regressor. 
In addition to each groups beta value (for BMI) I'm interested in the beta 
value of the interaction (ie diagnosis x BMI). I was wondering how do i go 
about obtaining this? Would I have to create a new matrix with the interaction 
term included in it?

If so would the analysis essentially be one group with the diagnosis x BMI 
interaction term plus the three co-variates?
If you are using an FSGD file and have used DODS, then you can create an 
interaction contrast. Send me your fsgd file if you want further help
Yes I was using DODS approach for this analysis, I've attached my FSGD file to 
this email.

You have 2 groups and 4 coviariates so 10 regressors. The dx BMI interaction 
would need a contrast matrix
0 0 1 -1 0 0 ... the rest 0s
BTW, sex should not be a covariate. You really need to have four groups, 
P-male, P-female, HC-male, and HC-female (which would change the contrast above)
Also, I would normalize the age and ICV

Thanks for the correction I'll update my matrix accordingly to four groups and 
normalize the variables! The contrast matrix I ran was actually the same you 
suggested however it pastes an array of beta values for each 10 regressors. 
However, I was interested in obtaining a beta value that represents the 
interaction.



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Re: [Freesurfer] Mean thickness values from sig.mgh

[Greve, Douglas N.,Ph.D.]

you will have to create a binary mask from the sig map by thresholding at a 
given level, eg,
mri_binarize --i sig.mgh --min 2 --o sig.bin2.mgh
Then run
mri_segstats --i y.mgh --seg sig.bin2.mgh --id 1 --avgwf y.bin2.dat
where y.mgh is the --y input to mri_glmfit
--id 1 means to take the forground of sig.bin2.mgh
y.bin2.dat will be a text file with the mean of y for each subject in the 
binarized map



On 1/22/2020 9:32 AM, Amrita Bedi wrote:

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Hello Freesurfer developers,

I wanted to extract mean thickness values of all participants from the 
uncorrected significance maps obtained from mri glmfit for structural data 
instead of extracting it from the corrected maps from glmfit sim. Is there a 
way to do this?

Thank you.

Amrita



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Re: [Freesurfer] global measures of volume bug

[Greve, Douglas N.,Ph.D.]

On 1/22/2020 2:54 AM, Christian Krog Tamnes wrote:

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Dear FS experts,

I came across this post about a bug related to global measures of volume from 
version 6.0:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed

I have two questions that I hope someone can clarify:
1) This bug does not affect measures of cortical thickness or area, or specific 
subcortical volumes, correct?
Correct
2) For longitudinally processed data, is it sufficient to run the proposed 
solution (recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 
-wmparc –balabels) on the longitudinal data, or do we need to first do it on 
the cross-sectionally processed data?
You do not need to run it on the cross-sectional data, just the longitudinal 
data

Best regards,
Christian




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Re: [Freesurfer] Qdec error

[Greve, Douglas N.,Ph.D.]

I would normalize all the variables. Eg, column 2 is nearly identical to column 
1

On 1/22/2020 1:03 AM, vittal korann wrote:

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Dear Douglas

I did normalize ICV values. This is something else I guess.

With regards
Vittal



On Tue, Jan 21, 2020 at 6:09 PM vittal korann 
mailto:vittalkor...@gmail.com>> wrote:
Dear FreeSurfer experts

I ran QDEC and got the following error.

Design matrix --
 1.0   1.04000  -1.38574   2.0   29.0   19.0;
 1.0   1.04000  -0.55066   2.0   35.0   19.0;
 1.0   1.03000   2.31721   2.0   23.0   14.0;
 1.0   1.03000  -0.22919   2.0   23.0   16.0;
 1.0   1.03000  -2.69688  -2.0   28.0   19.0;
 1.0   1.01000   0.84981  -2.0   22.0   19.0;
 1.0   1.01000   0.43845   2.0   36.0   21.0;
 1.0   1.06000   1.32888   2.0   28.0   17.0;
 1.0   1.02000   0.52292   2.0   34.0   22.0;
 1.0   1.02000   0.18104   2.0   32.0   17.0;
 1.0   1.03000  -0.33783  -2.0   32.0   22.0;
 1.0   1.04000   0.65805   2.0   30.0   17.0;
 1.0   1.03000   1.21888   2.0   37.0   10.0;
 1.0   1.02000   2.11598   2.0   29.0   10.0;
 1.0   1.02000  -0.02853   2.0   27.0   16.0;
 1.0   1.04000   0.21777   2.0   36.0   16.0;
 1.0   1.01000   0.30821   2.0   29.0   15.0;
 1.0   1.03000  -0.69389   2.0   30.0   12.0;
 1.0   1.04000   0.44792   2.0   23.0   15.0;
 1.0   1.03000   0.15876   2.0   28.0   15.0;
 1.0   1.02000  -1.05796   2.0   36.0   10.0;
 1.0   1.05000  -1.51878   2.0   32.0   15.0;
 1.0   1.03000  -0.91870  -2.0   30.0   15.0;

ERROR: matrix is ill-conditioned or badly scaled, condno = 68200

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y /usr/local/freesurfer/subjects/qdec/Untitled/y.mgh 
--fsgd /usr/local/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir 
/usr/local/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label 
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label --C 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
 --C 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-Vein_Avg_tort-Cor.mat
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=4.795832 (col 1), Max=145.206757 (col 5)
 The scale is much different between columns 1 and 5, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.

Any help would be appreciated!

With regards
Korann




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Re: [Freesurfer] Extract specific LGI and Volume values

[Greve, Douglas N.,Ph.D.]

I'm guessing that there is something wrong with the label. Can you send it?

On 1/21/2020 8:08 PM, Tien Pham wrote:

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Thank you for your e-mail.
I also could not load the label in freeview. The terminal showed the following 
error:

2020-01-22 09:56:18.064 Freeview[51338:303] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:
2020-01-22 09:56:26.655 Freeview[51338:303] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:
freadFloat: fread failed
freadFloat: fread failed

This error was still showing like it never end until I close freeview.

 I draw the ROI in qdec, then add selection to ROI , and save the current 
label. That was how I created the label.
I am looking forward to hearing from you. Thank you.

On Wed, Jan 22, 2020 at 12:17 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
You can try freeview, but there might be something wrong with the label. How 
was it created?

On 1/16/2020 11:51 PM, Tien Pham wrote:

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Thank you for your help.
I cannot load the label on surface, this is the error:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% qdec

Reading /applications/freesurfer/tktools/tkUtils.tcl

Using /applications/freesurfer/lib/tcl/fsgdfPlot.tcl
qdec.bin(41334,0xa15971a8) malloc: *** mach_vm_map(size=114944) failed 
(error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRISalloc(15124178, 76): could not allocate faces
Cannot allocate memory

What do you mean how many point? How do I find it?

On Fri, Jan 17, 2020 at 1:17 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Is the label valid? Can you load it on a surface? How many points are in it?

On 1/16/2020 9:51 PM, Tien Pham wrote:

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Thank you for your e-mail.
It seems I got another error. This is what it showed in terminal:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats --i 
lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label 
--id 1 --sum sum.dat
sysname  Darwin
hostname toyama-no-iMac.local
machine  x86_64
user toyama
UseRobust  0
Constructing seg from label
Segmentation fault

Could you help me please?

On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Sorry, it should have been --sum instead of --o
the subject name is subject_id
--id 1 just means to take the vertices in the label (--id 0 would mean to take 
the background)

On 1/16/2020 7:07 PM, Tien Pham wrote:

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Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id '' 
flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in my 
dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 
--o sum.dat

The mean value will be in the "Mean" column of the sum.dat


On 1/14/2020 7:08 PM, Tien Pham wrote:

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Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI 
changes in my data set with two time points using longitudinal pipeline. Now I 
would like to extract the regional LGI and gray matter volume in my 
longitudinal results using QDEC to draw the ROIs which is showed significant 
differences, label it and map to all subjects. Then I get the LGI value of the 
ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% 
mris_anatomical_stats -l lh.frontoinsula.label \
? -t lh.pial_lgi \
? -b \
? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
limiting computations to label lh.frontoinsula.label.
using thickness file lh.pial_lgi.
reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...
reading input pial surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...
reading input white surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature

Re: [Freesurfer] Qdec and TkSurfer input boxes

[Greve, Douglas N.,Ph.D.]

I don't know. Can you reconfigure to English to do a test?

On 1/21/2020 12:14 PM, Marcos Martins da Silva wrote:

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FreeSurfer 6 over CentOS 7. I have the same problem with 5.3 too. One more 
information: CentOS 7 is configured as PT-br instead of English. Could it be 
the reason?

Em ter, 21 de jan de 2020 12:29, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> escreveu:
Which version of FS are you using? I don't have this problem in v6 or dev. What 
OS are you using?


On 1/17/2020 9:09 AM, Marcos Martins da Silva wrote:

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Thank you, Doug! Yes, there is an option to load a fsgd file in Freeview, but 
when you try to use this option Freeview closes wirh error. I tried to use the 
y.fsgd generated by Qdec process. This file works great when you use it in 
TkSurfer, but not in Freeview. I just need to get the thickness measure from my 
subjects at a particular vertex: vtmax. I can use mri-segstats to get average 
thickness from clusters, but not the thickness from each subject at vtmax. And 
I know if the input boxes were working I could get the scatter plot from vtmax, 
so I guess there is a function inside both Qdec and TkSurfer to return this 
information.

Em qui, 16 de jan de 2020 20:36, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> escreveu:
Sorry, qdec and tksurfer are becoming (have become?) obsolete. I think you can 
load an fsgd file in freeview

On 1/15/2020 11:02 AM, Marcos Martins da Silva wrote:

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Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with 
input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click 
inside the box and even select the content but it seems read only: I can't 
change it. So it is impossible to see the scatter plot from a specific vertex 
inputing its number. Any clue about what happened and how to fix it? Thank you 
for your attention.



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Re: [Freesurfer] Hippocampal subfield validation

[Iglesias Gonzalez, Juan E.]

Dear Dawn,
Thank you very much for your interest in the tool, but we do not have such a 
dataset, sorry! Having said that, I don’t think the alveus should make a big 
difference in Dice scores…
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of "Dawn C. Matthews" 

Reply-To: Freesurfer support list 
Date: Thursday, 23 January 2020 at 20:36
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfield validation


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Dear Freesurfer Team,
Thank you for your work on the segmentation and analysis tools that have been 
provided through Freesurfer and that have been used so widely. We are wondering 
if there is a T1 image data set available for which manual delineation of the 
boundaries of the hippocampal subfield summation has been performed, and 
whether the images and masks might be available for DICE comparison to the 
masks and volume produced by FS in users’ hands? We note that the subfield 
summation does not include the alveus and therefore direct comparison to masks 
generated using standard manual hippocampal segmentation protocols is not 
straightforward.
With thanks and best regards,
Dawn Matthews


Dawn C. Matthews
CEO, ADM Diagnostics, Inc.
555 Skokie Blvd., Suite 500
Northbrook, Illinois  60062
dmatth...@admdx.com


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