Re: [Freesurfer] multi-slice timing correction

[Joseph Dien]

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Okay, I looked through the source code itself and I think I worked it out.

preproc-sess calls on stc-sess, passing it both the sdf and the ngroups flags.
stc-sess calls on stc.fsl, passing it both the sdf and the ngroups flags.
stc.fsl calls on slicetimer.  It uses the sdf flag if it has been set to a file 
name, otherwise it uses the other flags including ngroups to call on slicedelay 
to generate an sdf file which it then passes on to slicetimer.

So in other words, if an sdf file is provided, then the ngroups flag is ignored 
and does not need to be set.

Am I correct?  I’d like to make sure I’m doing this right.

Thanks again for this amazing toolset!

Joe

> On Jun 11, 2019, at 15:55, Joseph Dien  wrote:
> 
> External Email - Use Caution
> 
> 
> looking further into the archives, I see that the -sdf flag can be used.  I’m 
> still uncertain about the -ngroups flag.  I see at least a couple other users 
> have asked about this but I don’t see a response.  In the present case, if 
> there are 60 slices and they are accelerated by a factor of 6, does one 
> specify -ngroups 6 or -ngroups 10?
> 
> Joe
> 
>> On Jun 2, 2019, at 19:46, Joseph Dien > > wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Hi Doug,
>>I’m happy to see that FreeSurfer6 provides enhanced support for slice 
>> timing.  I’m trying to run it on some multi-slice data.  May I ask you for 
>> some guidance on how to use the new preproc-sess options?  As I understand 
>> it, I would specify “-ngroups 10” because the data were collected in ten 
>> groups of six slices at a time?  I’m not sure how to specify “-sliceorder”.  
>> Slice times are below.  Thanks for any help you can provide.
>> 
>> Joe
>> 
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 0
>> 877.5000
>> 502.5000
>> 125
>> 1005
>> 627.5000
>> 252.5000
>> 1130
>> 752.5000
>> 377.5000
>> 
>> 
>> 
>> Joseph Dien, PhD
>> Senior Research Scientist
>> Department of Human Development and Quantitative Methodology
>> University of Maryland, College Park
>> http://joedien.com 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 
> Joseph Dien, PhD
> Senior Research Scientist
> Department of Human Development and Quantitative Methodology
> University of Maryland, College Park
> http://joedien.com 
> ___
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Joseph Dien, PhD
Senior Research Scientist
Department of Human Development and Quantitative Methodology
University of Maryland, College Park
http://joedien.com

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Re: [Freesurfer] multi-slice timing correction

[Joseph Dien]

External Email - Use Caution

looking further into the archives, I see that the -sdf flag can be used.  I’m 
still uncertain about the -ngroups flag.  I see at least a couple other users 
have asked about this but I don’t see a response.  In the present case, if 
there are 60 slices and they are accelerated by a factor of 6, does one specify 
-ngroups 6 or -ngroups 10?

Joe

> On Jun 2, 2019, at 19:46, Joseph Dien  wrote:
> 
> External Email - Use Caution
> 
> 
> Hi Doug,
>I’m happy to see that FreeSurfer6 provides enhanced support for slice 
> timing.  I’m trying to run it on some multi-slice data.  May I ask you for 
> some guidance on how to use the new preproc-sess options?  As I understand 
> it, I would specify “-ngroups 10” because the data were collected in ten 
> groups of six slices at a time?  I’m not sure how to specify “-sliceorder”.  
> Slice times are below.  Thanks for any help you can provide.
> 
> Joe
> 
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 0
> 877.5000
> 502.5000
> 125
> 1005
> 627.5000
> 252.5000
> 1130
> 752.5000
> 377.5000
> 
> 
> 
> Joseph Dien, PhD
> Senior Research Scientist
> Department of Human Development and Quantitative Methodology
> University of Maryland, College Park
> http://joedien.com 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



Joseph Dien, PhD
Senior Research Scientist
Department of Human Development and Quantitative Methodology
University of Maryland, College Park
http://joedien.com

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[Freesurfer] mri_gtmpvc with amended aparc+aseg

[Albrecht, Daniel S.]

Hello,

I’ve been using PETSurfer for partial volume correction of PET images using the 
RBV option. I’m amending the parcellations/segmentations to add in 
extracortical areas of high PET signal (to prevent spill-in into the brain), 
and after adjusting the *ctab file this runs successfully.

However, I noticed the output resolution of the rbv.nii.gz image is the same as 
the input segmentation mask, not the expected 0.5mm iso. I’ve run a test 
incorporating the --rbv-res 0.5mm flag into the command line. The output 
rbv.nii.gz image is similar to the previous one (without the –rbv-res flag), 
again not as smooth as the typical output image.

Is it satisfactory to run the command with my amended seg image and the 
--rbv-res 0.5mm flag, and are there any additional recommendations for running 
PVC with an amended seg image?

Thanks very much,

Dan

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Re: [Freesurfer] hippocampal subfield as CONN seeds

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

This will be a little tricky. How did you do the registration to MNI space?

On 6/11/2019 1:36 AM, Nelson, Eric A wrote:

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Hi all,

I have successfully ran hippocampal subfields for a sample but would like to be 
able to use some of those subfields as seed regions in CONN. Is there a method 
I can use to convert the individual subfields to MNI space so I can import some 
of subject level subfields to an existing CONN project?

I thought using mri_vol2vol on the hippoSfLabels-T1.v10.mgz might be the best 
solution but get the following error

regio_read_mincxfm: No such file or directory
ERROR: could not read transforms/talairach.xfm

Best,

Eric



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Re: [Freesurfer] label a ROI

[Bruce Fischl]

Hi Francesca

sorry, not sure if this got answered, but you should be able to create 
surface-based ROIs and run the analysis on them.


cheers
Bruce


On Wed, 5 Jun 2019, Francesca Pentimalli wrote:



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Dear Bruce, 
Thank you very much for answering!

We are doing a study on correlating dyslexia, at an early stage, with various 
factors in children.
Specifically, our goal is to look at how the 12 regions of the brain, that I 
mentioned in the
previous email, play a role in the study. 

Up until now, I have done an mri_average of all the images and used the qdec 
interface to see how
cortical thickness and surface area vary with parameters such as gender, age 
and maternal education.
This produced interesting results but they get affected when the Monte Carlo 
correction is run on
the same. Further, I want to run the analysis specifically inside certain 
regions of interest. For
that purpose, I thought about creating the masks in freesurfer considering just 
the regions of
interest and  run the analysis in them. Is this a good way to go about this?

Thank you very much for your kind attention.

Best regards,

Francesca





Il giorno mer 5 giu 2019 alle ore 18:45 Bruce Fischl 
 ha scritto:
  Hi Francesca

  what analysis do you want to run?

  cheers
  Bruce
  On Wed, 5 Jun 2019, Francesca Pentimalli
  wrote:

  >
  > External Email - Use Caution
  >
  > Dear Freesurfer experts,
  >
  >
  > I am trying to create a mask and run the analysis into it considering 
just the
  following anatomical
  > regions:
  >
  >
  >  (1) inferior frontal gyrus pars opercularis (IFGOp)
  >
  >  (2) inferior frontal gyrus pars orbitalis (IFGOr)
  >
  >  (3) inferior frontal gyrus pars triangularis (IFGTr)
  >
  >  (4) Heschl3s gyrus (HG)
  >
  >  (5) the superior temporal gyrus (STG)
  >
  >  (6) planum polare (PP)
  >
  >  (7) planum temporale (PT)
  >
  >  (8) supramarginal gyrus (SMAR)
  >
  >  (9) angular gyrus (AG)
  >
  > (10) fusiform gyrus (FFG)
  >
  > (11) inferior occipital gyrus (IOG)
  >
  > (12) insula
  >
  >
  > Which technique do you suggest? Is there a good tutorial for it?
  > Thank you very very much!!
  >
  > Best regards,
  >
  > Francesca  Francesca Pentimalli Biscaretti di Ruffia Via S. Eufemia 3, 
35121 Padova
  (Italy)
  > Mobile: +39 3483862788
  > francesca.pentimallibiscarettidiruf...@studenti.unipd.it
  > fpentimalli...@gmail.com
  > fpe...@mit.edu
  > fp...@bu.edu
  >
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--
Francesca Pentimalli Biscaretti di Ruffia Via S. Eufemia 3, 35121 Padova (Italy)
Mobile: +39 3483862788
francesca.pentimallibiscarettidiruf...@studenti.unipd.it
fpentimalli...@gmail.com
fpe...@mit.edu
fp...@bu.edu

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[Freesurfer] Correlate Dose Distribution with Cortical Thickness Change

[Janneke Janssens]

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*We already send this email from a Medaustron email address but for some
reason the response was blocked and cannot be seen anymore*



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
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[Freesurfer] Cerebellum and brainstem mask

[Miguel Ángel Rivas Fernández]

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Dear Freesurfer devs,

I would like to exclude from the T1 image those voxels that correspond to
the cerebellum and brainstem. I tried to do this using the following
commands although I am not completely sure if they are the right ones:

1. Extract cerebellum and brain stem labels from the aseg.mgz file

mri_extract_labels aseg.mgz 45 46 47 6 7 8 16 cerebellum_brainstem.mgz


2. Binarize the mask

mri_binarize --i cerebellum_brainstem.mgz --o cerebellum_brainstem_mask.mgz
--min 0 --max 0


3. Convert the mask to native space

mri_convert -rl orig/001.mgz -rt nearest cerebellum_brainstem_mask.mgz
cerebellum_brainstem_mask.nii


Any help would be appreciated. Thanks in advance.


Best regards,


-- 
*Miguel Ángel Rivas Fernández*
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[Freesurfer] Yeo Atlas Download

[Aster, Hans-Christoph]

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Dear Freesurfer Team,

I cannot download the "Resting State Cortical Parcellation in nonlin MNI152 
space" with several machines. Is there something  wrong with the server? The 
error message is: Server Connection was reset.

Thank you in advance, kind regards
Hans

---

Dr. med. univ. Hans-Christoph Aster
Neurologische Klinik
Universitätsklinikum Würzburg
Josef-Schneider-Str. 11
D-97080 Würzburg
Tel. +49 931 201 23668
aste...@ukw.de
http://www.neurologie.ukw.de/

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