[Freesurfer] correlate dose distribution with cortical thickness change

[Janneke Janssens]

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Dear FreeSurfer Developers,


We are doing research on cortical changes after radiation therapy to the brain. 
We are trying to compare the thickness of the cortex at the beginning of the 
radiation (T0) and after one year of treatment (T1). Subsequently, we would 
like to correlate the thickness change to the dose given to the specific brain 
areas.

We ran the ‘recon-all’ commands for longitudinal data. All the commands 
executed without errors according to the log file.


“recon-all -all -i IM1.DCM -s Subj001_MR1”

“recon-all -all -i IM1.DCM -s Subj001_MR2”


“recon-all -base Subj001 -tp Subj001_MR1 -tp Subj001_MR2 –all”


“recon-all -long Subj001_MR1 Subj001 –all”

“recon-all -long Subj001_MR2 Subj001 –all”



We could find cortical changes and load them into qdec. However, the problem 
now is that we want to correlate the dose distribution to these thickness 
changes. We encounter the next issues:

  *   How to insert the dose files (DICOM-format) into FreeSurfer/qdec to make 
it part of the analysis?
 *   We have searched for instructions, both in the archives and in the 
tutorials, how to import the dose files into FreeSurfer but we cannot find any 
documentation. Does anybody have experience with loading dose-files into 
FreeSurfer software?
  *   How to execute statistical analysis within a subject? In this case, 
correlate thickness changes and dose distribution from one patient?
 *   In the tutorials and the archives we couldn’t find any within-subject 
analysis. Nevertheless, in the paper ‘Dose-Dependent Cortical Thinning After 
Partial Brain Irradiation in High-Grade Glioma’ of Karunamuni et al. (2016) 
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747044/) this type of analysis 
is done, so we know it is possible. We already contacted the authors of this 
paper but they do not respond.


The version of Freesurfer we are using is: 
Freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c on a macOS Mojave operating 
system.

Thank you very much in advance, it would be of great help if you could advise 
us regarding this experiment.

We are looking forward to your response.


Kind regards,

Janneke Janssens and Piotr Andrzejewski

E: janneke.janss...@medaustron.at

T: +43 2622 26 100 660
Disclaimer:
Please notice our E-Mail Disclaimer http://www.medaustron.at/email-disclaimer/

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Re: [Freesurfer] running recon -all and trac -all from different FreeSurfer home

[Costanza Gianni']

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Thank you Anastasia,
I'll try and let you know.

Costanza

Il mer 5 giu 2019, 18:36 Yendiki, Anastasia  ha
scritto:

> Hi Costanza - When you use "\" in a shell script to continue a command
> onto the next line, make sure that the "\" is the very last character of
> the line (see second to last entry in your bvec list.
>
>
> On a separate note, you'll have to specify the bval file(s).
>
>
> Best,
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Costanza Gianni' <
> costanza.gia...@uniroma1.it>
> *Sent:* Wednesday, June 5, 2019 9:27:12 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] running recon -all and trac -all from
> different FreeSurfer home
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> I've attached the configuration file.
>
> Best,
> Costanza
>
> Il giorno mer 5 giu 2019 alle ore 15:07 Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> ha scritto:
>
> Hi Costanza - can you please attach your configuration file?
>
> Best,
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Costanza Gianni' <
> costanza.gia...@uniroma1.it>
> *Sent:* Wednesday, June 5, 2019 6:49:02 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] running recon -all and trac -all from different
> FreeSurfer home
>
>
> External Email - Use Caution
>
> Hello, FreeSurfer Developers,
>
> I'm trying to run trac -all (I prepared the configuration file following
> the instructions from v. 5.3) on a set of subjects already processed with
> recon -all in another computer with a different FREESURFER HOME, and I'm
> getting this error:
>
> Too many ('s.
> INFO: SUBJECTS_DIR is /home/costanza/extra/PET/PET
> INFO: Diffusion root is /home/costanza/extra/PET/PET
> Actual FREESURFER_HOME /home/costanza/freesurfer
> INFO: FreeSurfer build stamps do not match
> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> /home/costanza/freesurfer/bin/dmri_motion: Command not found.
> /home/costanza/freesurfer/bin/dmri_group: error while loading shared
> libraries: libnetcdf.so.6: cannot open shared object file: No such file or
> directory
> INFO: current FREESURFER_HOME does not match that of previous processing.
> Current: /home/costanza/freesurfer
> Previous:
> /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013
> dcmlist: Subscript out of range.
>
> I've searched the list and I couldn't find any similar error. Do you think
> the main problem is running commands from different FREESURFER HOME?
>
> 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> 2) Ubuntu 14.04.5 LTS
> 3) umane -a Linux wks4 3.13.0-166-generic #216-Ubuntu SMP Thu Feb 7
> 14:07:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>
> Thanks a lot for your help,
>
> Costanza
>
> --
> Costanza Giannì, MD
> Radiologist
> PhD student
> Sapienza University, Rome
> +39 348 711 8987
>
>
>
> ___
> *Il tuo 5 diventa 1000*
> Fai crescere la tua università
> Dona il 5 per mille alla Sapienza
> Codice fiscale: *80209930587*
>
> https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille
>
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>
>
>
> --
> Costanza Giannì, MD
> Radiologist
> PhD student
> Sapienza University, Rome
> +39 348 711 8987
>
>
>
> ___
> *Il tuo 5 diventa 1000*
> Fai crescere la tua università
> Dona il 5 per mille alla Sapienza
> Codice fiscale: *80209930587*
>
> https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille
>
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Fai 
crescere la tua università
Dona il 5 per mille alla Sapienza
Codice 
fiscale: *80209930587*

https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille
 


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[Freesurfer] scan acquisition date from recon all

[Boris Rauchmann]

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Dear all,

is there any way to find the scan acquisition date in the recon-all log?

Thanks,
Boris
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[Freesurfer] A Question Regarding the Command "mris_divide_pacellation"

[Maedeh Khalilian]

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Dear experts,
I use the file "lh/rh.aparc.annot" and a splitfile as the inputs of the 
command "mris_divide_parcellation" in order to have a parcellation with more 
regions.
Now I have a question: for example if in my splitfile I write 4 in front of 
the region "precuneus", how does it divide this region into 4 subregions? Is 
it based on a specific pattern or it is random? I mean if I repeat this 
command line 100 times with the same splitfile, will the results be the 
same? I would be grateful if you could help me.
Best regards,
Maedeh,


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Re: [Freesurfer] A Question Regarding the Command "mris_divide_pacellation"

[Bruce Fischl]

Hi Maedeh

I think it divides along the maximum variance eigen-axis, so should be 
repeatable.


cheers
Bruce
On Thu, 6 Jun 2019, Maedeh Khalilian wrote:



External Email - Use Caution

Dear experts,
I use the file "lh/rh.aparc.annot" and a splitfile as the inputs of the command
"mris_divide_parcellation" in order to have a parcellation with more regions.
Now I have a question: for example if in my splitfile I write 4 in front of the region 
"precuneus",
how does it divide this region into 4 subregions? Is it based on a specific 
pattern or it is random?
I mean if I repeat this command line 100 times with the same splitfile, will 
the results be the
same? I would be grateful if you could help me.
Best regards,
Maedeh,
 
 

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[Freesurfer] A Question Regarding the Command "mris_divide_pacellation"

[Maedeh Khalilian]

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Dear Bruce,
Thank u very much for replying. sorry I'm still a little bit doubtful, just 
as a confirmation:  by repeatable you mean I can repeat it and every time 
get a a new result? or every time the result will be the same?
Best,
Maedeh,


Hi Maedeh

I think it divides along the maximum variance eigen-axis, so should be 
repeatable.

cheers
Bruce
On Thu, 6 Jun 2019, Maedeh Khalilian wrote:

> 
> External Email - Use Caution
> 
> Dear experts,
> I use the file "lh/rh.aparc.annot" and a splitfile as the inputs of?the 
command
> "mris_divide_parcellation" in order to have a parcellation with more 
regions.
> Now I have a question: for example if in my splitfile I write 4 in front 
of the region "precuneus",
> how does it divide this region?into 4 subregions? Is it based on a 
specific pattern or it is random?
> I mean if I?repeat this command line 100 times with the same splitfile, 
will?the results be the
> same??I would be grateful if you could help me.
> Best regards,
> Maedeh,___
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[Freesurfer] Surface Mesh Mapped to Voxels

[Raunak Swarnkar]

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Hi

I am using freesurfer to extract just the cortical surface mesh. Next, I
want to map each vertex on the surface mesh to its corresponding voxel in
the volumetric atlas. Any help how to go forward with it?

Regards
Raunak Swarnkar
Visiting Student Researcher - Summer 2019
Dept. of Mathematics & Statisitcs, uOttawa
MSc Cognitive Science Student, IIT Gandhinagar
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[Freesurfer] CSF MASK

[Marina Fernández]

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Dear Freesurfer experts,

Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?

Thank you in advance.

Best regards,
Marina.
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[Freesurfer] CSF MASK

[Marina Fernández]

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Dear Freesurfer experts,

Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?

Thank you in advance.

Best regards,
Marina.
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Re: [Freesurfer] A Question Regarding the Command "mris_divide_pacellation"

[Bruce Fischl]

it should be the same I would think
cheers
Bruce
On Thu, 6 Jun 2019, Maedeh Khalilian 
wrote:




External Email - Use Caution

Dear Bruce,
Thank u very much for replying. sorry I'm still a little bit doubtful, just as 
a confirmation:  by
repeatable you mean I can repeat it and every time get a a new result? or every 
time the result will
be the same?
Best,
Maedeh,
 
Hi Maedeh

I think it divides along the maximum variance eigen-axis, so should be 
repeatable.

cheers
Bruce
On Thu, 6 Jun 2019, Maedeh Khalilian wrote:

> 
> External Email - Use Caution
> 
> Dear experts,
> I use the file "lh/rh.aparc.annot" and a splitfile as the inputs of?the 
command
> "mris_divide_parcellation" in order to have a parcellation with more regions.
> Now I have a question: for example if in my splitfile I write 4 in front of 
the region
"precuneus",
> how does it divide this region?into 4 subregions? Is it based on a specific 
pattern or it is
random?
> I mean if I?repeat this command line 100 times with the same splitfile, 
will?the results be the
> same??I would be grateful if you could help me.
> Best regards,
> Maedeh,

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Re: [Freesurfer] Surface Mesh Mapped to Voxels

[Bruce Fischl]

Hi Raunak

this page should have the info you need:

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

cheers
Bruce
On Thu, 6 Jun 
2019, Raunak Swarnkar 
wrote:




External Email - Use Caution

Hi
I am using freesurfer to extract just the cortical surface mesh. Next, I want 
to map each vertex on
the surface mesh to its corresponding voxel in the volumetric atlas. Any help 
how to go forward with
it?

RegardsRaunak Swarnkar
Visiting Student Researcher - Summer 2019
Dept. of Mathematics & Statisitcs, uOttawa
MSc Cognitive Science Student, IIT Gandhinagar

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Re: [Freesurfer] CSF MASK

[Bruce Fischl]

Hi Marina

not with our default tools. Koen (ccd) has something that will generate 
this, but it is not run by default.


cheers
Bruce


On Thu, 6 Jun 2019, Marina Fernández wrote:



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Dear Freesurfer experts,
Is there any way to obtain a CSF mask in Freesurfer similar to that 
obtained with the SPM segmentation (see attached)? 

Thank you in advance.

Best regards,
Marina. 

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[Freesurfer] FW: Query regarding way to quote covariates in fsgd file

[Basavaraju, Rakshathi]

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Hi all FS users,
I have the basic doubt of including age and gender as co-variates for a 
cortical thickness comparison between 2 groups. I read extensively many mails 
answering these questions but still could not get a satisfactory answer for the 
question.
As I have 2 discrete variables i.e. Group with 2 levels and gender with 2 
levels and one continuous variable of age my contrast matrix should be like 
this:
[0 0 0 0 0 0 0 0] which is [malegroup1 femalegroup1 malegroup2 femalegroup2 
age.malegroup1 age.femalegroup1 age.malegroup2 age.femalegroup2]
I understood that if I have to test the effect of only the groups my contrast 
matrix should be:
[0.5 0.5 -0.5 -0.5 0 0 0 0]
What should be my contrast matrix if I have to include age and gender as 
covariates respectively? I know gender cannot be included as columns of 1s and 
0s by my reading of previous mails.
In one of the mail I read that if we want to test for interaction of group and 
gender (disregarding effect of age) the contrast matrix file should be:
[0.5 -0.5 -0.5 0.5 0 0 0 0]
But is testing for gender as a covariate same as testing group*gender 
interaction? I do not feel so. Hence requesting you all to throw some clarity 
on this. If this is not the way to study gender as a covariate how else should 
the contrast matrix be written?
And regarding age should it be four 0.5s for the last 4 columns of the matrix 
if we want to study age as a covariate? Kindly let know.
Finally I want a contrast matrix that studies the group differences in cortical 
thickness covarying for the effect of age and gender. Kindly help me.

Thanks,
Dr. Rakshathi Basavaraju (MD Psychiatry)
Postdoctoral Research Scientist
Taub Institute
Columbia University Irving Medical Centre
622 West, 168th Street, New York - 10032
E-Mail: rb3...@cumc.columbia.edu
http://www.wellcomedbt.org/fellowsprofile/dr-rakshathi-basavaraju-288

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[Freesurfer] examining between group differences using DODS

[Avi Gharehgazlou]

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Hi experts,

I want to examine between-group differences in LGI controlling for age, sex
and surface area (all except sex demeaned).

To do so, I ran the DODS model on QDEC selecting:

- “diagnosis” and “sex” as discrete (fixed factors)

- “age” and “surface area” as nuisance factors

- And selected this question à “Does the average pial_lgi,
accounting for sex, differ between TD and NDD? Nuissance factors: Age
Surface area”

1) I wanted to ask you what the significant results from the above analysis
means?

I was under the impression that the significant clusters represent clusters
where there are significant group differences in LGI while controlling for
age, surface area and sex.

But I am confused because I know from previous threads that you recommend
to run DODS to check for interactions first, and if there is no interaction
to then run DOSS to see differences between groups. So:

2) Do my significant results mean that I have an interaction between
diagnosis and sex OR diagnosis and age OR diagnosis and surface area?

3) Considering that I have an interaction, how do I now examine between-group
differences in LGI? Is what I have done (through the DODS model) correct?


I'd really appreciate your help,


Thanks so much,


Avi
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[Freesurfer] Confirmation regarding running GLM on command line stream

[Avi Gharehgazlou]

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Hi experts,



Will you please confirm below command lines I run to examine between group
differences in LGI? I have 3 questions listed.



I can’t run the below line, it gives an error:

mris_preproc --fsgd TDvsNDDageSAsex.fsgd --cache-in
lh.pial_lgi.fwhm0.fsaverage --target fsaverage --hemi lh --meas pial_lgi
--out lh.pial_lgi.0.mgh

mris_preproc --fsgd TDvsNDDageSAsex.fsgd --cache-in
rh.pial_lgi.fwhm0.fsaverage --target fsaverage --hemi rh --meas pial_lgi
--out rh.pial_lgi.0.mgh



Therefore, I run the below line instead - although I know it’s for uncached
data and I have already ran qcache for my subjects (using: recon-all -s
101031_01 -qcache -measure pial_lgi)



mris_preproc --fsgd ASDvsADHD.txt --target fsaverage --hemi lh --meas
pial_lgi --out lh.pial_lgi.mgh

mri_surf2surf --hemi lh --s fsaverage --sval lh.pial_lgi.mgh --fwhm 0
--cortex --tval lh.pial_lgi.0.mgh

# I run above line separately for right hemisphere

1.   Do I have to write “cortex” in above command line or not?

2.   Is it okay to run this command line considering that qcache has
already been run on all my subjects?

3.   I’ve ran qcache (and above command line) multiple times on each
subject in my data. Is this ok? Or does this mess up anything?

To test for main effect of group, I ran below line:

mri_glmfit --y lh.pial_lgi.0.mgh --fsgd ASDvsADHD.txt dods --C
betweengroupdifferencecontrollingforageSAsex.mtx --C
agebydiagnosisinteraction.mtx --surf fsaverage lh --cortex --glmdir
lh.ASDvsADHD.glmdir

mri_glmfit --y rh.pial_lgi.0.mgh --fsgd ASDvsADHD.txt dods --C
betweengroupdifferencecontrollingforageSAsex.mtx --C
agebydiagnosisinteraction.mtx --surf fsaverage rh --cortex --glmdir
rh.ASDvsADHD.glmdir



To correct for multiple comparisons using monte carlo:

mri_glmfit-sim --glmdir lh.ASDvsADHD.glmdir --cache 1.3 abs --cwp 0.05
--2spaces

mri_glmfit-sim --glmdir rh.ASDvsADHD.glmdir --cache 1.3 abs --cwp 0.05
--2spaces


I'd really appreciate your soon reply,


Thanks so much for all your support,


Avi
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Re: [Freesurfer] scan acquisition date from recon all

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

If you gave recon-all a dicom as an input, then it might be in there due to the 
conversion.

On 6/6/2019 5:24 AM, Boris Rauchmann wrote:

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Dear all,

is there any way to find the scan acquisition date in the recon-all log?

Thanks,
Boris



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Re: [Freesurfer] CSF MASK

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

No, not currently (next version)

On 6/6/2019 12:57 PM, Marina Fernández wrote:

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Dear Freesurfer experts,

Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?

Thank you in advance.

Best regards,
Marina.



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