[Freesurfer] FreeSurfer for mouse brain

[Heidi Foo]

Dear FreeSurfer experts,

I am currently trying to run FreeSurfer on a set of mouse brains and I have
a few questions about it:

1. Is it possible to generate 2D surfaces from a set of structural scans on
mouse brain in FreeSurfer?

2. Do the individual steps like Normalisation, Segmentation, Tessellation,
etc rely on the Talairach space?

3. Is there any way that I can replace the Talairach atlas that the steps
use in the root directories or codes?

Thank you!

Best Regards,
Heidi Foo
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Re: [Freesurfer] Functional Overlap Map

[Douglas N. Greve]

I'm not entirely sure what you are doing. It sounds like you have 3 
different conditions and want to find out where the activation for all 
conditions overlaps. But what you have done is to combine all conditions 
into a single condition, so you are seeing where the average activation 
is, which is different than the overlap (and why it looks to have to 
much of an extent). To do what you want to do, you should model each 
condition as a separate condition in mkanalysis (ie, -nconditions 3 and 
change your paradigm file), set up 3 contrasts (one for each condition, 
ie, -a 1, -a 2, -a 3), then you will need to do a conjunction analysis 
(mri_concat con1/sig.nii.gz con2/sig.nii.gz con3/sig.nii.gz --conjunct 
--o conjunction.nii.gz). You can then view the conjunction with freeview 
(or tksurfer/tkmedit)


On 03/20/2018 06:30 PM, nm644 wrote:
>
> Hello Freesurfer experts,
>
> My question may have already been solved in a previous thread. I have 
> three runs of block-design bold scans. All three are quite similar. 
> They all have only 2 blocks, one for rest and one for task. I’m trying 
> to create a functional map that displays where the functional 
> activation of these three runs overlap. I used the code below with no 
> errors:
>
> preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh 
> -mni305 -fwhm 5 -per-run
>
> mkanalysis-sess \
>
>   -fsd bold -stc up -surface fsaverage lh -fwhm 5 \
>
> -event-related -paradigm para.tsv -nconditions 1 \
>
>   -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \
>
>   -analysis TaskOverlap.lh  -per-run -force
>
> mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1
>
> selxavg3-sess -s subj01 -analysis TaskOverlap.lh
>
> And to display:
>
> tksurfer-sess -s subj01 \
>
> -analysis TaskOverlap.lh \
>
> -c con1
>
> Or
>
> tksurfer-sess -s subj01 \
>
> -analysis TaskOverlap.lh \
>
> -c con1 -map fsig
>
> The problem is that when I view the output it seems that there’s far 
> more activation than there should be when trying to find mutual 
> overlap between the three tasks. If anyone has any suggestions it 
> would be much appreciated.
>
> Have a great day!
>
>
>
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[Freesurfer] Functional Overlap Map

[nm644]

Hello Freesurfer experts,

My question may have already been solved in a previous thread. I have three 
runs of block-design bold scans. All three are quite similar. They all have 
only 2 blocks, one for rest and one for task. I’m trying to create a functional 
map that displays where the functional activation of these three runs overlap. 
I used the code below with no errors:

preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 
5 -per-run

mkanalysis-sess \
  -fsd bold -stc up -surface fsaverage lh -fwhm 5 \
  -event-related -paradigm para.tsv -nconditions 1 \
  -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \
  -analysis TaskOverlap.lh  -per-run -force

mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1

selxavg3-sess -s subj01 -analysis TaskOverlap.lh

And to display:
tksurfer-sess -s subj01 \
-analysis TaskOverlap.lh \
-c con1

Or

tksurfer-sess -s subj01 \
-analysis TaskOverlap.lh \
-c con1 -map fsig

The problem is that when I view the output it seems that there’s far more 
activation than there should be when trying to find mutual overlap between the 
three tasks. If anyone has any suggestions it would be much appreciated.

Have a great day!

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Re: [Freesurfer] Registering functional data between scan sessions

[David Beeler]

Awesome, thanks Doug!


For clarity, I got it working with:


bbregister --s  --mov  --reg day1func-to-day1anat.lta 
--init-fsl --bold

bbregister --s  --mov  --reg day2func-to-day2anat.lta 
--init-fsl --bold

bbregister --s  --mov $SUBJECTS_DIR//mri/brain.mgz 
--reg day1anat-to-day2anat.lta --init-fsl --t1

mri_concatenate_lta day1func-to-day1anat.lta day1anat-to-day2anat.lta 
test/day1func-to-day2anat.lta

mri_concatenate_lta -invert2 day1func-to-day2anat.lta day2func-to-day2anat.lta 
day1func-to-day2func.lta

mri_vol2vol --mov  --targ  --reg 
day1func-to-day2func.lta --o day1func-in-day2func.nii.gz


Cheers,

DB
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Re: [Freesurfer] Cortical volume parcellation

[Mark Wagshul]

Bruce,

I haven't used tksurfer before, but it seems like the best way to do what I 
need would be to edit the pre-existing labels in the fsaverage aparc+aseg 
image.  What I want is almost exclusively from the superior and rostral-middle 
frontal labels already there, I just need to limit their extent.  Just wanted 
to know what you thought of this approach (although, to be honest, this might 
take some time, just to learn how to use tksurfer).

Thanks,

Mark 


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu


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-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, March 18, 2018 3:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume parcellation

Hi Mark

the easiest thing to do would be to draw the label you want on the fsaverage 
surface, then use mri_label2label to map from there to each of your individual 
subjects

cheers
Bruce
On Sun, 18 Mar 2018, Mark Wagshul wrote:

> Hi.  I'm new to using Freesurfer.  We are using the parc + aseg segmentation, 
> but would like to extract functionally-relevant cortical regions, which I 
> don't see specified in the output.  Specifically, I would like to calculate 
> cortical thickness of the dorsal pre-frontal cortex, which overlap with parts 
> of the cortical parcellations that I'm currently getting.  Is there any way 
> to do this within Freesurfer, or will I have to use another atlas (e.g. We 
> could generate this on the Mni template, morph it into subject space and 
> dilate to ensure that it captures the entire cortical surface).
>
> Thanks for any advice you can provide on this.
>
> Best,
>
> Mark
> ___
> Mark Wagshul, PhD
> Albert Einstein College of Medicine
> Bronx, NY
>
> Sent from my iPhone
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[Freesurfer] POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING

[Xiaosong He]

 POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING THOMAS JEFFERSON UNIVERSITY/
SIDNEY KIMMEL MEDICAL COLLEGE, PHILA., PA.
The Department of Neurology at Thomas Jefferson University/Jefferson
Medical College has an opening for a Two-Year Postdoctoral Research
Fellowship in Neuroimaging focusing on both clinical brain mapping and
primary cognitive neuroscience investigations. The emphasis in our
neuroimaging program is on cognitive and behavioral network organization
and plasticity in neurologic disorders such as epilepsy. The lab focuses on
the use of advanced network neuroscience measures to understand seizure
networks and cognitive reorganization in epilepsy, and has had recent
publications in Brian, Neurology, and Epilepsia, with some also prompting
complimentary peer reviews. The lab is part of the Jefferson Comprehensive
Epilepsy Center, an internationally-known epilepsy surgery program.
Presurgical brain mapping studies are undertaken (MRI volumetrics,
task-fMRI, resting state functional connectivity, diffusion imaging,
neuropsychological assessment, electrophysiology/electrocortical
stimulation) as well as post-surgical neuroimaging studies investigating
clinical, cognitive, and behavioral outcomes. The pre-surgical brain
mapping studies are conducted on a regular basis, utilized in image-guided
surgery, and then made available for research. Studies in brain recovery
and the cognitive reorganization of language and memory functions are
emphasized, utilizing rich multi-modal datasets for the investigation of
both cognitive and pathologic (e.g., seizure) networks. Thomas Jefferson
University provides a high-level interdisciplinary research environment
with grand rounds, seminars, case conferences, and opportunities to
collaborate with faculty across departments such as neurosurgery and
radiology. Successful applicants must have a strong background in image
processing and analysis using programs such as MATLAB, SPM, Freesurfer, and
FSL with a strong interest in clinical neuroimaging and cognitive
neuroscience. Applicants must have a Ph.D. or MD in neuroscience,
biomedical engineering, statistics, neurology, neuropsychology, radiology,
or related field. Interested applicants should send a CV and cover letter
stating experience and interests, 2-3 peer-reviewed publications.
Anticipated start date is 7/1/18, but is flexible. Contact: Joseph I.
Tracy, Ph.D., ABPP(CN). Director, Cognitive Neuroscience and Brain Mapping
Laboratory, Thomas Jefferson Univ./Sidney Kimmel Medical Coll., Jefferson
Hospital for Neuroscience, 901 Walnut Street, Suite #447, Phila., PA 19107,
phone:#215-955-4661, e-mail: joseph.tr...@jefferson.edu.
Thomas Jefferson University and Hospitals is an Equal Opportunity Employer.
Jefferson values diversity and encourages applications from women, members
of minority groups, LGBTQ individuals, disabled individuals, and veterans.
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[Freesurfer] Brainstem registration

[Chungmin Han]

Dear whomever it may concern,

I'm Chungmin, a graduate research assistant in University of Texas at
Austin,
I'm fairly new to using freesurfer, I'd appreciate to get some advice on
what I'm facing,

*I've had this posted but for some reason lost track of it so I'm uploading
it again.*

I have fMRI limited FOV collected on brainstem + little cerebellum/visual
area,
I've tried SPM manual registration to MNI space, falls in 1-2mm (1-2
voxels) away from accurate registering brainstem correctly, I have T1
mprage in 1mm resolution, but seems T1 registration to MNI space has a bit
of error around "Brainstem" area.

is there a way to create transformation matrix *optimized to fit brainstem
in MNI space*?
Registering cortical region slightly bit wrong is okay to me at this
moment,

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

I've noticed this has been posted pretty recently, but would like to figure
out how to align in standard space for comparison.

I've also thought of inverse registering from MNI to each native space,
however, if the transformation focuses on maximizing registration on the
cortical level (T1) I don't think inverse registration solves the issue,

The area that I'm interested in is lateral nuclei, reticular formation etc.
so it would rather be focused on the midbrain, not even at the level of
diencephalon,


and Additional question, would using fsaverage be more beneficial over
MNI152 registration?
in terms of brainstem warped into the standard space more accurately.

Thank you in advance :)
Best

PS How do you reply to your own question after someone replies?


Chungmin

Chungmin Han

Graduate Research Assistant
The University of Texas at Austin
204 E. Dean Keeton St Austin TX 78712
Mobile: 512-717-1671
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Re: [Freesurfer] mir_vol2surface registration file error

[Charlotte Grosse Wiesmann]

Hi Srishti,

your volume maps are in some template space right? (the template you can open 
them on) This might be some MNI template space, but not necessarily the same 
the other people have used. You can register these to one another, e.g. with 
ANTS:

Start ANTS in terminal

> ants.sh 3 TheirTemplate.nii YourTemplate.nii

This will give you a transformation matrix (xxx_Warp.nii and xxx_Affine.txt) 
that you can use to warp your ROIs to their template space:

> WarpImageMultiTransform 3 YourROI.nii output_image -R TheirTemplate.nii 
> xxx_Warp.nii.gz xxx_Affine.txt

Then you can open the output image (Your ROI warped to their template space) 
and their ROI on their template with fslview, or compute any analysis to 
compare them.

I don't understand why you would use mri_vol2surf if you only want the volume. 
What this function does is to map the volume to the surface, so if you don't 
need the surface you don't need the fct.

Best

Charlotte



- Original Message -
From: "23srishtigoel" <23srishtig...@gmail.com>
To: "wiesmann" 
Sent: Tuesday, March 20, 2018 2:16:21 PM
Subject: Re: [Freesurfer] mir_vol2surface registration file error

Hi Charlotte,

Thank you so much for your detailed response, I really appreciate it.

With respect to your third point, comparing volume maps, what exactly do
you mean by registering our template to their MNI152 template? What exactly
will be our template file?
I was using the same mri_Vol2surf for comparing the volume maps as well,
for example:

mri_vol2surf --src negative_allsocial.nii --mni152reg --hemi lh --o
./neg_allsocial.nii --projfrac 0.5


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Mon, Mar 19, 2018 at 6:14 AM, Charlotte Grosse Wiesmann <
wiesm...@cbs.mpg.de> wrote:

> Hi Shrishti,
>
> 1) by recon-all I meant recon-all in the freesurfer pipeline (
> https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all ) to reconstruct the
> subject's cortical surfaces because if I got you right you have the maps on
> the surface (SN_like_cortical_lh.gz) and in the volume. If you only want to
> compare the maps in the volume you can skip this part I only compare the
> volume maps.
>
> 2) As far as I know with mri_vol2surf and tksurfer you can use a number of
> different formats including .nii (if not you can convert with mri_convert)
>
> 3) I'm not sure I understand your question. Make sure both of your volume
> maps are registered to the same MNI152 template. (Best is if you ask the
> people who gave you their maps to also give you the template. Then you can
> register your template to that template (e.g., using ANTS) and the
> transformation matrix you obtain to map your maps onto the other
> template.)  If both volume maps are in the same space you can both open
> them with fslview on the template they have been registered to (fslview
> template.nii map1.nii map2.nii) and compare them visually.
>
> Best
>
> Charlotte
>
>
>
> - Original Message -
> From: "23srishtigoel" <23srishtig...@gmail.com>
> To: "wiesmann" 
> Sent: Sunday, March 18, 2018 5:37:40 PM
> Subject: Re: [Freesurfer] mir_vol2surface registration file error
>
> Hi Charlotte,
>
> Thank you so much for your help, I really appreciate it and this is super
> helpful for me. I just want to clarify a couple small thing
>
> 1) By running recon-all on that subject do you mean reconstructing that
> subject's DICOM basically?
> 2) I notice that the extension you are using is .mgh so would I have to
> convert the volume maps (which is SN_like_cortical.nii) into mgh/mgz/gz as
> well?
> 3) Also, would you be able to elaborate a little on how to view the volumes
> on the MNI. I have used fslview and I think I know how to map our volume
> maps on the MNI152 volume space but I am not sure what would be the best
> way to use fslview to view it.
>
> Thanks once again!
>
> Best,
> Srishti
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> skype: srishti.goel12
>
>
> On Sun, Mar 18, 2018 at 10:55 AM, Charlotte Grosse Wiesmann <
> wiesm...@cbs.mpg.de> wrote:
>
> > Hi Srishti,
> >
> > I had a similar problem recently, so I will try to help. To compare your
> > maps with the surface maps SN_like_cortical_lh.gz of the others you need
> to
> > map your volume to the surface of the same subject they are using.
> >
> > That is, you first have to run recon-all on that subject (unless they
> gave
> > you the link to the subject folder for which recon-all has already been
> > run. Say, the name of the subject folder is SUBJECT-ID).
> >
> > Then, you need to map your volume to the surface of that subject:
> > mri_vol2surf --src negative_allsocial_proportion.nii --regheader
> > SUBJECT-ID --hemi lh --o ./neg_allsocial_lh.mgh [more options]

Re: [Freesurfer] Hippocampal Subfield Atlas

[Iglesias Gonzalez, Eugenio]

It’s in $FREESURFER_HOME/average/HippoSF/atlas
But it’s not straightforward to visualize it…
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Roberto Medeiros de 
Souza 
Reply-To: Freesurfer support list 
Date: Tuesday, 20 March 2018 at 17:49
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal Subfield Atlas

Hello,

Does anyone know in which freesurfer folder I find the atlas corresponding to 
the following publication: "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MR"?

Thanks,
Roberto
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[Freesurfer] Hippocampal Subfield Atlas

[Roberto Medeiros de Souza]

Hello,

Does anyone know in which freesurfer folder I find the atlas corresponding
to the following publication: "A computational atlas of the hippocampal
formation using ex vivo, ultra-high resolution MRI: Application to adaptive
segmentation of in vivo MR"?

Thanks,
Roberto
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Re: [Freesurfer] [FSFAST]

[Douglas Greve]

Sorry, yes you can use an A-B blocked paradigm. Run mkanalysis-sess 
-help to get more info



On 3/20/18 4:28 AM, Walid Yassin wrote:

Hello all,

I would like to pose my question again in case it got missed.

Thank you.

WY

On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin > wrote:


Hi Doug,

Is it possible to run retinotopy-like analysis to reveal areas in
the brain responsible for a certain phase of a presented stimuli?
Say, instead of presenting 0 - 360 degrees of rotating wedge per
cycle, we would like to present arbitrary scale of 0 - 100 of a
particular stimulus feature, that does not necessarily differ in
their retinotopic locations.

We thought, if we pretend that scale-0 is equivalent to a wedge of
0 degree, and scale-50 is equivalent to a wedge of 180 degrees,
and so on, we would be able to map the cortical area corresponding
to each value of the scale.
However, the retinotopy protocol of freesurfer requires the input
of a stimulus type “e.g. polar or eccen” and direction “e.g. pos
or neg”, so our analysis won’t work as we intend.

Running Freesurfer v5.3.0

Thank you

Walid




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Re: [Freesurfer] [FSFAST]

[Walid Yassin]

Hello all,

I would like to pose my question again in case it got missed.

Thank you.

WY

On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin 
wrote:

> Hi Doug,
>
> Is it possible to run retinotopy-like analysis to reveal areas in the
> brain responsible for a certain phase of a presented stimuli?
> Say, instead of presenting 0 - 360 degrees of rotating wedge per cycle, we
> would like to present arbitrary scale of 0 - 100 of a particular stimulus
> feature, that does not necessarily differ in their retinotopic locations.
>
> We thought, if we pretend that scale-0 is equivalent to a wedge of 0
> degree, and scale-50 is equivalent to a wedge of 180 degrees, and so on, we
> would be able to map the cortical area corresponding to each value of the
> scale.
> However, the retinotopy protocol of freesurfer requires the input of a
> stimulus type “e.g. polar or eccen” and direction “e.g. pos or neg”, so our
> analysis won’t work as we intend.
>
> Running Freesurfer v5.3.0
>
> Thank you
>
> Walid
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