Re: [Freesurfer] AAL parcellation for Freesurfer

[Bastian Cheng]

External Email - Use Caution

great, that worked, thank you!

after that I recon-all'ed the colin27 brain so that I could use vol2label
and label2annot for a lh.aal.annot and rh.aal.annot.


On Thu, 28 May 2020 at 17:53, Douglas N. Greve 
wrote:

> Not that I know of. I played around a little with them. Below are my notes
> on getting it onto the colin27 brain. Good luck!
>
> Downloaded AAL from http://www.gin.cnrs.fr/spip.php?article217,
> specifically http://www.gin.cnrs.fr/AAL/aal_for_SPM8.tar.gz
>
> The ROIs are in ROI_MNI_V4.nii, but they need to be left right
> reversed
>
> mri_convert ROI_MNI_V4.nii ROI_MNI_V4.lrrev.nii --left-right-reverse-pix
>
> To map to the raw colin27 brain
>
>  mri_label2vol --seg ROI_MNI_V4.lrrev.nii --temp colin27_t1_tal_lin.nii \
>--regheader colin27_t1_tal_lin.nii --o  ROI_MNI_V4.anat.lrrev.nii
>
>
> On 5/28/2020 9:37 AM, Bastian Cheng wrote:
>
> External Email - Use Caution
> Dear all,
>
> does anyone know if there is a surface parcellation file based on the AAL
> for freesurfer? I am aware that I could recon-all the MNI brain and project
> the atlas on the surface. (but maybe someone already did that)
>
> I spend some time googeling this, but haven't found it, therefore my
> question.
>
> all the best,
> Bastian
>
>
> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
>  Virenfrei.
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[Freesurfer] AAL parcellation for Freesurfer

[Bastian Cheng]

External Email - Use Caution

Dear all,

does anyone know if there is a surface parcellation file based on the AAL
for freesurfer? I am aware that I could recon-all the MNI brain and project
the atlas on the surface. (but maybe someone already did that)

I spend some time googeling this, but haven't found it, therefore my
question.

all the best,
Bastian


Virenfrei.
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[Freesurfer] Create surface Label from MNI152 Coordinate

[Bastian Cheng]

Dear Freesurfer Experts.

Is there a  way to create a freesurfer surface label from entering a
MNI152 coordinate? I would like to extract cortical thickness data
from fMRI peak activation coordinates.

I am aware that I can use tcl with tksurfer:

mar_vertex X 1
labl_new_from_marked_vertices
labl_dilate

However as far as I know I can only input vertex numbers, not coordinates.

Any helpt would be greatly appreciated!
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[Freesurfer] Create surface label from MNI152 Coordinate.

[Bastian Cheng]

Dear Freesurfer Experts.

Is there a  way to create a freesurfer surface label from entering a
MNI152 coordinate?

I am aware that I can use tcl with tksurfer:

mar_vertex X 1
labl_new_from_marked_vertices
labl_dilate

However as far as I know I can only input vertex numbers, not coordinates.

Any helpt would be greatly appreciated!

Bastian
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Re: [Freesurfer] registration of intraparietal sulcus

[Bastian Cheng]

too sad!

Thank you anyway - I'll try my luck with matlab.

Bastian.

On 30 April 2016 at 17:43, Douglas Greve  wrote:
> I don't have anything to do this.
>
> On 4/30/16 10:26 AM, Bruce Fischl wrote:
>> not that I know of, but Doug might have something. I would do it in matlab
>> I guess
>>
>> On Sat, 30 Apr 2016, Bastian Cheng wrote:
>>
>>> Hi Bruce!
>>>
>>> sounds good, thank you!
>>>
>>> is there a specific command to do that? I would guess that I would
>>> have to mask the sulc image with my label (S-intrapariet_and_P_trans)
>>>
>>> Bastian
>>>
>>> On 29 April 2016 at 14:46, Bruce Fischl  wrote:
>>>> Hi Bastien
>>>>
>>>> maybe it would be easier and more accurate to extract the
>>>> S_inrapriet_and_P_trans then use sulc to remove any vertices that are < 0
>>>> (that is, are not sulcal)?
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>>
>>>> On Fri, 29 Apr 2016, Bastian Cheng
>>>> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> I am creating a hand-drawn label of the Intraparietal sulcus on fsaverge.
>>>>>
>>>>> When I register it to an individual brain (mri_label2label), the area
>>>>> is incorrectly registered and comprises adjacent brain structures that
>>>>> I am not interested in analyzing (specially the neighboring sulci).
>>>>>
>>>>> I know that registration works with my data in general, since other
>>>>> regions (manually drawn on fsaverage, i.e. various pre-motor areas)
>>>>> are correctly registered.
>>>>>
>>>>> is there any bias or "reduced" accuracy when registering regions of
>>>>> interest located at the parietal cortex?
>>>>>
>>>>> I am aware that aparc2009 comprises an area called
>>>>> "S_inrapriet_and_P_trans", but I've found that this label is not
>>>>> restricted to the sulcus (in individual segmentations).
>>>>>
>>>>> Any help would be appreciated!
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>>>>>
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Re: [Freesurfer] registration of intraparietal sulcus

[Bastian Cheng]

Hi Bruce!

sounds good, thank you!

is there a specific command to do that? I would guess that I would
have to mask the sulc image with my label (S-intrapariet_and_P_trans)

Bastian

On 29 April 2016 at 14:46, Bruce Fischl  wrote:
> Hi Bastien
>
> maybe it would be easier and more accurate to extract the
> S_inrapriet_and_P_trans then use sulc to remove any vertices that are < 0
> (that is, are not sulcal)?
>
> cheers
> Bruce
>
>
> On Fri, 29 Apr 2016, Bastian Cheng
> wrote:
>
>> Dear all,
>>
>> I am creating a hand-drawn label of the Intraparietal sulcus on fsaverge.
>>
>> When I register it to an individual brain (mri_label2label), the area
>> is incorrectly registered and comprises adjacent brain structures that
>> I am not interested in analyzing (specially the neighboring sulci).
>>
>> I know that registration works with my data in general, since other
>> regions (manually drawn on fsaverage, i.e. various pre-motor areas)
>> are correctly registered.
>>
>> is there any bias or "reduced" accuracy when registering regions of
>> interest located at the parietal cortex?
>>
>> I am aware that aparc2009 comprises an area called
>> "S_inrapriet_and_P_trans", but I've found that this label is not
>> restricted to the sulcus (in individual segmentations).
>>
>> Any help would be appreciated!
>> ___
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>>
>>
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[Freesurfer] registration of intraparietal sulcus

[Bastian Cheng]

Dear all,

I am creating a hand-drawn label of the Intraparietal sulcus on fsaverge.

When I register it to an individual brain (mri_label2label), the area
is incorrectly registered and comprises adjacent brain structures that
I am not interested in analyzing (specially the neighboring sulci).

I know that registration works with my data in general, since other
regions (manually drawn on fsaverage, i.e. various pre-motor areas)
are correctly registered.

is there any bias or "reduced" accuracy when registering regions of
interest located at the parietal cortex?

I am aware that aparc2009 comprises an area called
"S_inrapriet_and_P_trans", but I've found that this label is not
restricted to the sulcus (in individual segmentations).

Any help would be appreciated!
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[Freesurfer] Intraparietal sulcus - incorrect registrations

[Bastian Cheng]

Dear all,

I am creating a hand-drawn label of the Intraparietal sulcus on fsaverge.

When I register it to an individual brain (mri_label2label), the area
is incorrectly registered and comprises adjacent brain structures that
I am not interested in analyzing (specially the neighboring sulci).

I know that registration works with my data in general, since other
regions (manually drawn on fsaverage, i.e. various pre-motor areas)
are correctly registered.

is there any bias or "reduced" accuracy when registering regions of
interest located at the parietal cortex?

I am aware that aparc2009 comprises an area called
"S_inrapriet_and_P_trans", but I've found that this label is not
restricted to the sulcus (in individual segmentations).

Any help would be appreciated!

Bastian
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[Freesurfer] Flipping Surface .mgh file to opposite hemisphere via fsav_sym

[Bastian Cheng]

Dear Freesurfer-Experts,

I am trying to flip surface files (.mgh) from right to left.

I have read your instructions concerning xhemi and performed
registration to fsaverage_sym:

foreach subject (subjectlist)
  surfreg --s $subject --t fsaverage_sym --lh
  surfreg --s $subject --t fsaverage_sym --lh --xhemi
end

I would now like to flip surfaces containing fMRI-values (initally on
the right hemisphere) to the left hemisphere for statistics in a
common space.

How do I achieve this?

I have tried using mri_surf2surf with different side (--srchemi rh
--trghemi lh) using the fsaverage_sym as subject.

However would I not need a registration file rh.lh.sphere.reg for
that? It doesn't work with using the left side as targed either
(results are shifted and do not match the location on the original
hemisphere)

What am I doing wrong?

I dont want to compare the right with the left hemisphere (I simply
want to have all affected surfaces on one side of the brain).

any help would be appreciated!

Bastian
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Re: [Freesurfer] Create surface Labels of equal size

[Bastian Cheng]

Hi Bruce, thank you!

I looked up all commands here:
http://freesurfer.net/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference

I guess what I should do is

1) mark vertex at coordinate
2) create label at marked vertex
3) maybe dilate the label.

does this sound right?

On 4 November 2014 23:24, Bruce Fischl  wrote:
> Hi Bastian
>
> you should be able to do this with a tcl script in tksurfer. Take a look
> at the ones we distribute for some examples
>
> cheers
> Bruce
> On Tue, 4 Nov 2014, Bastian
> Cheng wrote:
>
>> Dear Freesurfers,
>>
>> I would like to mark the brain surface (fsaverage) for an illustration
>> of stimulation areas (TMS).
>>
>> I have calculated coordinates in Vertex RAS and Vertex Talairach. They
>> are correctly located on the fsaverage surface in tksurfer.
>>
>> Is there a way to create labels of equal sizes at those coordinates?
>> Ideally by using a script (since I have to mark them in 50 patients).
>>
>> this is purely for illustrative purposes. All coordinates are in
>> fasaverage space.
>>
>> Any help would be appreciated,
>> Bastian
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>>
>>
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[Freesurfer] Create surface Labels of equal size

[Bastian Cheng]

Dear Freesurfers,

I would like to mark the brain surface (fsaverage) for an illustration
of stimulation areas (TMS).

I have calculated coordinates in Vertex RAS and Vertex Talairach. They
are correctly located on the fsaverage surface in tksurfer.

Is there a way to create labels of equal sizes at those coordinates?
Ideally by using a script (since I have to mark them in 50 patients).

this is purely for illustrative purposes. All coordinates are in
fasaverage space.

Any help would be appreciated,
Bastian
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Re: [Freesurfer] Flip ROI in fsaverage / mris_left_right_register

[Bastian Cheng]

great, thank you!!

On 12 August 2014 17:11, Douglas N Greve  wrote:
>
> I've refreshed those links, try now
> doug
>
> On 08/12/2014 09:40 AM, Bastian Cheng wrote:
>> Dear Freesurfers,
>>
>> I am trying to flip an overlay (.mgh) to the contralateral hemisphere.
>>
>> The overlay is in fsaverage-space.
>> I am using it only for visualization (and not doing any statistics).
>>
>> I noticed that there was a program that could achieve this:
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_left_right_register.centos5
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg.centos5
>>
>> However it is not online anymore.
>>
>> Would this still be the right way to do it?
>>
>> Best regards,
>> Bastian
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>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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[Freesurfer] Flip ROI in fsaverage / mris_left_right_register

[Bastian Cheng]

Dear Freesurfers,

I am trying to flip an overlay (.mgh) to the contralateral hemisphere.

The overlay is in fsaverage-space.
I am using it only for visualization (and not doing any statistics).

I noticed that there was a program that could achieve this:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_left_right_register.centos5
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg.centos5

However it is not online anymore.

Would this still be the right way to do it?

Best regards,
Bastian
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[Freesurfer] Flipped Hemisphere longitudinal analysis

[Bastian Cheng]

Dear Freesurfers,

Has anyone accomplished analysis of longitudinal cortex changes in a
dataset with "flipped" hemispheres?

I am currently struggling with data from stroke patients, half of them
with lesions on the right, half of them on the left side of the brain.

What I am planning: flip all healthy hemispheres to left and perform
longitud. analysis of cortical thickness change on that (helthy)
hemisphere.

I have read the notes on Surface-based Interhemispheric Registration
(xhemi) and most of the comments here. It seems to me that this would
allow me to compare both hemisph. sides at ONE timepoint. (but not
actually analyzing ONE (flipped) hemisphere over time).

Any help to point me in the right direction is greatly appreciated!

Bastian
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Re: [Freesurfer] Mask custom ROI with automated parcellation (aparc)

[Bastian Cheng]

works perfectly, thank you!

On 28 July 2014 19:27, Douglas N Greve  wrote:
>
> Does mri_mask work?
>
> On 07/28/2014 12:50 PM, Bastian Cheng wrote:
>> Thank you, Douglas!
>>
>> Is there a way to mask my functional ROI with these binarized aparc ROIs?
>>
>> I guess what I want to do is:  ROIfunctional *
>> ROI_precentral_binarized > masked ROIfunctional limted to precentral
>> region
>>
>> best regards,
>> Bastian.
>>
>> On 28 July 2014 18:25, Douglas N Greve  wrote:
>>> Try using mri_binarize on the aparc+aseg.mgz volume (aparc+aseg has the
>>> same ROIs as aparc but in volume format). You can map this into your
>>> functional space.
>>> doug
>>>
>>> On 07/25/2014 06:29 AM, Bastian Cheng wrote:
>>>> Dear Freesurfers,
>>>>
>>>> Is there a way to mask a custom ROI (or label) with a volume / label
>>>> from automated parcellations?
>>>>
>>>> I have an overlay with fMRI activations and am only interested in the
>>>> precentral cortex (as segmented in rh.aparc).
>>>>
>>>> I could do masking either on the label level (fMRI activation label *
>>>> rh.precentral.label)
>>>> OR on a volume level (fMRI ROI volume * rh.precentral volume)
>>>>
>>>> ultimately, I would only be interested in surface thickness of my fMRI
>>>> hotspots limited to the precentral cortex.
>>>>
>>>> So the most elegant way would be if there were a function in
>>>> mri_segstats that allows outputs of thickness values to be "sorted" by
>>>> the automated parcellation.
>>>>
>>>> But any help leading there is appreciated!
>>>>
>>>> Best,
>>>> Bastian
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>>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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Re: [Freesurfer] Mask custom ROI with automated parcellation (aparc)

[Bastian Cheng]

Thank you, Douglas!

Is there a way to mask my functional ROI with these binarized aparc ROIs?

I guess what I want to do is:  ROIfunctional *
ROI_precentral_binarized > masked ROIfunctional limted to precentral
region

best regards,
Bastian.

On 28 July 2014 18:25, Douglas N Greve  wrote:
>
> Try using mri_binarize on the aparc+aseg.mgz volume (aparc+aseg has the
> same ROIs as aparc but in volume format). You can map this into your
> functional space.
> doug
>
> On 07/25/2014 06:29 AM, Bastian Cheng wrote:
>> Dear Freesurfers,
>>
>> Is there a way to mask a custom ROI (or label) with a volume / label
>> from automated parcellations?
>>
>> I have an overlay with fMRI activations and am only interested in the
>> precentral cortex (as segmented in rh.aparc).
>>
>> I could do masking either on the label level (fMRI activation label *
>> rh.precentral.label)
>> OR on a volume level (fMRI ROI volume * rh.precentral volume)
>>
>> ultimately, I would only be interested in surface thickness of my fMRI
>> hotspots limited to the precentral cortex.
>>
>> So the most elegant way would be if there were a function in
>> mri_segstats that allows outputs of thickness values to be "sorted" by
>> the automated parcellation.
>>
>> But any help leading there is appreciated!
>>
>> Best,
>> Bastian
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>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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[Freesurfer] Mask custom ROI with automated parcellation (aparc)

[Bastian Cheng]

Dear Freesurfers,

Is there a way to mask a custom ROI (or label) with a volume / label
from automated parcellations?

I have an overlay with fMRI activations and am only interested in the
precentral cortex (as segmented in rh.aparc).

I could do masking either on the label level (fMRI activation label *
rh.precentral.label)
OR on a volume level (fMRI ROI volume * rh.precentral volume)

ultimately, I would only be interested in surface thickness of my fMRI
hotspots limited to the precentral cortex.

So the most elegant way would be if there were a function in
mri_segstats that allows outputs of thickness values to be "sorted" by
the automated parcellation.

But any help leading there is appreciated!

Best,
Bastian
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Re: [Freesurfer] Convert volume 2 Label

[Bastian Cheng]

Stupid me!

I just found what I need: mri_cor2label. It does exactly what I want:

"A utility to sample a volume onto the surface, then create a label of
all super-threshold points
regardless of whether they are connected or not"

I failed to recognize that I would have to binarize my fMRI
activations first using mri_binarize (and selecting an intensity
threshold).

This binarized volume files then goes into mri_cor2label using "--id 1".

works perfectly.

Sorry for this.
Bastian.




On 24 July 2014 17:25, Bruce Fischl  wrote:
> Hi Bastian
>
> can you explain further what you would like? A utility to sample a volume
> onto the surface, then create a label of all super-threshold points
> regardless of whether they are connected or not?
>
> cheers
> Bruce
>
> On Thu, 24 Jul 2014,
> Bastian Cheng wrote:
>
>> Dear Freesurfer-Experts,
>>
>> Is there an automated way to convert an overlay volume to a label file?
>> I guess I would look for a command called "vol2label".
>>
>> I am currently projecting volume files (fMRI activiation hotspots) to
>> surfaces (mri_vol2surf): this works nicely.
>>
>> However I then would have to define labels manually (using "custom
>> fill") by clicking on all (unconnected) spots on my surface.
>>
>> Please excuse any redundancies, I have not found a good solution in
>> the forum yet.
>>
>> Best regards,
>> Bastian.
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>>
>>
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> at
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[Freesurfer] Convert volume 2 Label

[Bastian Cheng]

Dear Freesurfer-Experts,

Is there an automated way to convert an overlay volume to a label file?
I guess I would look for a command called "vol2label".

I am currently projecting volume files (fMRI activiation hotspots) to
surfaces (mri_vol2surf): this works nicely.

However I then would have to define labels manually (using "custom
fill") by clicking on all (unconnected) spots on my surface.

Please excuse any redundancies, I have not found a good solution in
the forum yet.

Best regards,
Bastian.
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Re: [Freesurfer] Thickness measurements on longitudinal data set

[Bastian Cheng]

Sounds great, will try that!
Again, thank you very much for your help!
Bastian.

On 22 July 2014 01:53, Martin Reuter  wrote:
> Hi Bastian,
>
> yes, lta are the (here rigid) transformations (dat files are deprecated).
>
> you can use mri_convert -at 
>
> or mri_vol2vol for mapping images.
>
> I think, however, you are not interested in mapping images, but in ROI's
> on the surface.
> You can do the following:
>
> - draw/create the ROI in the base and use it on all the tp1.long.base
> etc.  (surfaces are in alignment).
> - draw/create the ROI in the tp1.long.base and use it on all ohter time
> points directly (again this works as surfaces are in alignment)
> - map things non-linearly with mri_surf2surf
>
> You won't need the lta files for any of this.
>
> Best, Martin
>
> On 07/19/2014 01:45 AM, Bastian Cheng wrote:
>> Thank you for clarification, Martin!
>>
>> Will do so and also try registration of  base >> TP1.long etc.
>>
>> Does FS create registration files (.dat) for this purpose
>> automatically? I found some *.lta files in the /mri/transfers folder
>> of the base image but am not sure how to apply them (maybe
>> tkregister2?)
>>
>> best regards,
>> Bastian
>>
>> On 18 July 2014 23:00, Martin Reuter  wrote:
>>> Hi Bastian,
>>>
>>> use the longitudinal base for it. Also, once your ROI is in that space
>>> you can simply apply it in each long as they are in the same space as
>>> the base. The registration of base >> TP1.long etc. probably only
>>> changes results very little.
>>>
>>> Best, Martin
>>>
>>>
>>> On 07/18/2014 10:45 AM, Bastian Cheng wrote:
>>>> Dear Freesurfer-Experts,
>>>>
>>>> I am currently trying to measure Cortical Thickness of a
>>>> Volume-defined ROI in a patient measured at 4 timepoints.
>>>>
>>>> Basically, I am interested in a ROI resulting from fMRI activation
>>>> measured on Timepoint 1.
>>>> I would then like to get thickness values in the same ROI for all
>>>> Timepoints 1-4.
>>>>
>>>> I have read the instructions here:
>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>>>> this works.
>>>>
>>>> now, my idea is:
>>>>
>>>> ROI from TP1 >> register to base image of longit. recon. ("base")
>>>> ROI from base >> TP1.long (from long recon)
>>>> ROI from base >> TP2.long (from long recon)
>>>> ROI from base >> TP3 long (from long recon)
>>>> ROI from base >> TP4.long (from long recon)
>>>>
>>>> OR should I simpy map my ROI to fsaverage and project it back all
>>>> individual timepoints?
>>>> ROI from TP1 >> register to fsaverage
>>>> ROI from fsaverage >> TP1 (not from long recon)
>>>> ROI from fsaverage >> TP2 (not from long recon)
>>>> etc.
>>>>
>>>> I understand that registration using the long. recon is more robust...
>>>>
>>>> Best regards,
>>>> Bastian
>>>> ___
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>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>> --
>>> Martin Reuter, Ph.D.
>>>
>>> Instructor in Neurology
>>> Harvard Medical School
>>> Assistant in Neuroscience
>>> Dept. of Radiology, Massachusetts General Hospital
>>> Dept. of Neurology, Massachusetts General Hospital
>>> Research Affiliate
>>> Computer Science and Artificial Intelligence Lab,
>>> Dept. of Electrical Engineering and Computer Science,
>>> Massachusetts Institute of Technology
>>>
>>> A.A.Martinos Center for Biomedical Imaging
>>> 149 Thirteenth Street, Suite 2301
>>> Charlestown, MA 02129
>>>
>>> Phone: +1-617-724-5652
>>> Email:
>>>  mreu...@nmr.mgh.harvard.edu
>>>  reu...@mit.edu
>>> Web  : http://reuter.mit.edu
>>>
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>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. I

Re: [Freesurfer] Thickness measurements on longitudinal data set

[Bastian Cheng]

Thank you for clarification, Martin!

Will do so and also try registration of  base >> TP1.long etc.

Does FS create registration files (.dat) for this purpose
automatically? I found some *.lta files in the /mri/transfers folder
of the base image but am not sure how to apply them (maybe
tkregister2?)

best regards,
Bastian

On 18 July 2014 23:00, Martin Reuter  wrote:
> Hi Bastian,
>
> use the longitudinal base for it. Also, once your ROI is in that space
> you can simply apply it in each long as they are in the same space as
> the base. The registration of base >> TP1.long etc. probably only
> changes results very little.
>
> Best, Martin
>
>
> On 07/18/2014 10:45 AM, Bastian Cheng wrote:
>> Dear Freesurfer-Experts,
>>
>> I am currently trying to measure Cortical Thickness of a
>> Volume-defined ROI in a patient measured at 4 timepoints.
>>
>> Basically, I am interested in a ROI resulting from fMRI activation
>> measured on Timepoint 1.
>> I would then like to get thickness values in the same ROI for all
>> Timepoints 1-4.
>>
>> I have read the instructions here:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>> this works.
>>
>> now, my idea is:
>>
>> ROI from TP1 >> register to base image of longit. recon. ("base")
>> ROI from base >> TP1.long (from long recon)
>> ROI from base >> TP2.long (from long recon)
>> ROI from base >> TP3 long (from long recon)
>> ROI from base >> TP4.long (from long recon)
>>
>> OR should I simpy map my ROI to fsaverage and project it back all
>> individual timepoints?
>> ROI from TP1 >> register to fsaverage
>> ROI from fsaverage >> TP1 (not from long recon)
>> ROI from fsaverage >> TP2 (not from long recon)
>> etc.
>>
>> I understand that registration using the long. recon is more robust...
>>
>> Best regards,
>> Bastian
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Martin Reuter, Ph.D.
>
> Instructor in Neurology
>Harvard Medical School
> Assistant in Neuroscience
>Dept. of Radiology, Massachusetts General Hospital
>Dept. of Neurology, Massachusetts General Hospital
> Research Affiliate
>Computer Science and Artificial Intelligence Lab,
>Dept. of Electrical Engineering and Computer Science,
>Massachusetts Institute of Technology
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
> mreu...@nmr.mgh.harvard.edu
> reu...@mit.edu
> Web  : http://reuter.mit.edu
>
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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[Freesurfer] Thickness measurements on longitudinal data set

[Bastian Cheng]

Dear Freesurfer-Experts,

I am currently trying to measure Cortical Thickness of a
Volume-defined ROI in a patient measured at 4 timepoints.

Basically, I am interested in a ROI resulting from fMRI activation
measured on Timepoint 1.
I would then like to get thickness values in the same ROI for all
Timepoints 1-4.

I have read the instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
this works.

now, my idea is:

ROI from TP1 >> register to base image of longit. recon. ("base")
ROI from base >> TP1.long (from long recon)
ROI from base >> TP2.long (from long recon)
ROI from base >> TP3 long (from long recon)
ROI from base >> TP4.long (from long recon)

OR should I simpy map my ROI to fsaverage and project it back all
individual timepoints?
ROI from TP1 >> register to fsaverage
ROI from fsaverage >> TP1 (not from long recon)
ROI from fsaverage >> TP2 (not from long recon)
etc.

I understand that registration using the long. recon is more robust...

Best regards,
Bastian
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Re: [Freesurfer] Freesurfer gifti-Surface in Matlab

[Bastian Cheng]

Problem solved!

took some effort trying everything out, but finally found a simple
solution by transforming everything into MNI

Here's how to convert from surface RAS to mni305

mni305ras = X*S*inv(K)*ras
X = talairach.xfm
S = scanner vox2ras (mri_info --vox2ras orig.mgz)
K = tkreg vox2ras (mri_info --vox2ras-tkr orig.mgz)
ras = surface ras from gifti file.

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






On 3 June 2014 09:08, Bastian Cheng  wrote:
> Hi Nick,
>
> again thank you your help! That works nicely.
>
> Where to I find the transformation matrix to register my structural
> volume data to the gii. surface file?
>
> I found two matrices in the lh.white.gii (), but not sure
> if it fits.
>
> I have to use the volume scan and gii suface in matlab for
> localization and source reconstruction of EEG data (that's why I can't
> use freeview).
>
> Bastian
>
>
> On 2 June 2014 20:50, Nick Schmansky, MGH  wrote:
>> Bastian,
>>
>> Are you using freeview to display the surface?  If so, you will need to
>> get the newest freeview.bin, which is here:
>>
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/
>>
>> this has been updated to read the new volume geometry info now included
>> in the lh.white.gii file, so that it aligns with the volume (via the
>> c_ras info).
>>
>> Nick
>>
>>
>> On Mon, 2014-06-02 at 12:10 +0200, Bastian Cheng wrote:
>>> Hi,
>>>
>>> Ok, thank you!
>>>
>>> One additional follow up:
>>>
>>> Once I converted the lh.white (freesurfer) to the lh.white.gii
>>> (gifti), the converted surface (.gii) does not fit on the structural
>>> scan from freesurfer anymore (neither brain.mgz or orig.mgz or
>>> nu.omz).
>>>
>>> How can I register my freesurfer structural data to the new gifti surface?
>>>
>>> I have noticed that a transformation matrix is inserted in the gifti
>>> file, but have not figured out in which space the image is transformed
>>> to..
>>>
>>> maybe you could help me clarify that.
>>>
>>> Best,
>>> Bastian.
>>>
>>> On 29 May 2014 17:25, Bruce Fischl  wrote:
>>> > Hi Bastian
>>> >
>>> > do you mean a surface that is only a piece of th original surface? You can
>>> > use label2patch for that, but I'm not sure if we can convert patches to
>>> > gifti. You should ask the FSL crew about label2surf though - we can't help
>>> > with that.
>>> >
>>> > cheers
>>> > Bruce
>>> >
>>> >
>>> > On Thu,
>>> > 29 May 2014, Bastian Cheng wrote:
>>> >
>>> >> Hi Nick,
>>> >>
>>> >> That works PERFECTLY! Thank you so much, it has been a big help!
>>> >>
>>> >> I hope I may ask you another question:
>>> >>
>>> >> I am actually trying to convert each freesurfer-label (from
>>> >> aparc.annot) into separate surfaces (not gifti-labels)
>>> >>
>>> >> So ideally I would convert lh.precentral.label > lh.precentral.gii.
>>> >>
>>> >> I have used the command "label2surf", Part of FSL (build 504). (and I
>>> >> have used the "new" gifti lh.white created with your updated version
>>> >> as the input surface)
>>> >>
>>> >> However, the output gifti does not open in matlab (instead shows the
>>> >> same error message seen before).
>>> >>
>>> >> Now I would guess that whatever changes you made to mris_convert would
>>> >> have to be applied to "label2surf" as well. I have noticed some
>>> >> changes in the gifti files with your new mris_convert command.
>>> >> However, I'm not so familiar with the gifti file structure.
>>> >>
>>> >> Maybe I could ask you to have a look into this?
>>> >>
>>> >> Also, If there is a easier way to achieve my goal any advise is welcome!
>>> >>
>>> >> Again, many thanks for your efforts so far!
>>> >> Bastian.
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> On 29 May 2014 02:05, Nick Schmansky, MGH  
>>> >> wrote:
>>> >>> Bastian,
>>> >>>
>>> >>> Hi

Re: [Freesurfer] Freesurfer gifti-Surface in Matlab

[Bastian Cheng]

Hi Nick,

again thank you your help! That works nicely.

Where to I find the transformation matrix to register my structural
volume data to the gii. surface file?

I found two matrices in the lh.white.gii (), but not sure
if it fits.

I have to use the volume scan and gii suface in matlab for
localization and source reconstruction of EEG data (that's why I can't
use freeview).

Bastian


On 2 June 2014 20:50, Nick Schmansky, MGH  wrote:
> Bastian,
>
> Are you using freeview to display the surface?  If so, you will need to
> get the newest freeview.bin, which is here:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/
>
> this has been updated to read the new volume geometry info now included
> in the lh.white.gii file, so that it aligns with the volume (via the
> c_ras info).
>
> Nick
>
>
> On Mon, 2014-06-02 at 12:10 +0200, Bastian Cheng wrote:
>> Hi,
>>
>> Ok, thank you!
>>
>> One additional follow up:
>>
>> Once I converted the lh.white (freesurfer) to the lh.white.gii
>> (gifti), the converted surface (.gii) does not fit on the structural
>> scan from freesurfer anymore (neither brain.mgz or orig.mgz or
>> nu.omz).
>>
>> How can I register my freesurfer structural data to the new gifti surface?
>>
>> I have noticed that a transformation matrix is inserted in the gifti
>> file, but have not figured out in which space the image is transformed
>> to..
>>
>> maybe you could help me clarify that.
>>
>> Best,
>> Bastian.
>>
>> On 29 May 2014 17:25, Bruce Fischl  wrote:
>> > Hi Bastian
>> >
>> > do you mean a surface that is only a piece of th original surface? You can
>> > use label2patch for that, but I'm not sure if we can convert patches to
>> > gifti. You should ask the FSL crew about label2surf though - we can't help
>> > with that.
>> >
>> > cheers
>> > Bruce
>> >
>> >
>> > On Thu,
>> > 29 May 2014, Bastian Cheng wrote:
>> >
>> >> Hi Nick,
>> >>
>> >> That works PERFECTLY! Thank you so much, it has been a big help!
>> >>
>> >> I hope I may ask you another question:
>> >>
>> >> I am actually trying to convert each freesurfer-label (from
>> >> aparc.annot) into separate surfaces (not gifti-labels)
>> >>
>> >> So ideally I would convert lh.precentral.label > lh.precentral.gii.
>> >>
>> >> I have used the command "label2surf", Part of FSL (build 504). (and I
>> >> have used the "new" gifti lh.white created with your updated version
>> >> as the input surface)
>> >>
>> >> However, the output gifti does not open in matlab (instead shows the
>> >> same error message seen before).
>> >>
>> >> Now I would guess that whatever changes you made to mris_convert would
>> >> have to be applied to "label2surf" as well. I have noticed some
>> >> changes in the gifti files with your new mris_convert command.
>> >> However, I'm not so familiar with the gifti file structure.
>> >>
>> >> Maybe I could ask you to have a look into this?
>> >>
>> >> Also, If there is a easier way to achieve my goal any advise is welcome!
>> >>
>> >> Again, many thanks for your efforts so far!
>> >> Bastian.
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On 29 May 2014 02:05, Nick Schmansky, MGH  
>> >> wrote:
>> >>> Bastian,
>> >>>
>> >>> Hi, I've posted a new mris_convert which should solve the problem for
>> >>> you.  It's built for Centos 6, so if you need it for another platform,
>> >>> let me know.  It's here:
>> >>>
>> >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
>> >>>
>> >>> Nick
>> >>>
>> >>>
>> >>>
>> >>> On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote:
>> >>>> Dear Freesurfer-Experts,
>> >>>>
>> >>>> I would like to create gifti-surfaces to use in matlab.
>> >>>>
>> >>>> That's what I am doing so far (latest FS-Version):
>> >>>>
>> >>>> mris_convert lh.white lh.white.gii
>> >>>>
>> >>&

Re: [Freesurfer] Freesurfer gifti-Surface in Matlab

[Bastian Cheng]

Hi,

Ok, thank you!

One additional follow up:

Once I converted the lh.white (freesurfer) to the lh.white.gii
(gifti), the converted surface (.gii) does not fit on the structural
scan from freesurfer anymore (neither brain.mgz or orig.mgz or
nu.omz).

How can I register my freesurfer structural data to the new gifti surface?

I have noticed that a transformation matrix is inserted in the gifti
file, but have not figured out in which space the image is transformed
to..

maybe you could help me clarify that.

Best,
Bastian.

On 29 May 2014 17:25, Bruce Fischl  wrote:
> Hi Bastian
>
> do you mean a surface that is only a piece of th original surface? You can
> use label2patch for that, but I'm not sure if we can convert patches to
> gifti. You should ask the FSL crew about label2surf though - we can't help
> with that.
>
> cheers
> Bruce
>
>
> On Thu,
> 29 May 2014, Bastian Cheng wrote:
>
>> Hi Nick,
>>
>> That works PERFECTLY! Thank you so much, it has been a big help!
>>
>> I hope I may ask you another question:
>>
>> I am actually trying to convert each freesurfer-label (from
>> aparc.annot) into separate surfaces (not gifti-labels)
>>
>> So ideally I would convert lh.precentral.label > lh.precentral.gii.
>>
>> I have used the command "label2surf", Part of FSL (build 504). (and I
>> have used the "new" gifti lh.white created with your updated version
>> as the input surface)
>>
>> However, the output gifti does not open in matlab (instead shows the
>> same error message seen before).
>>
>> Now I would guess that whatever changes you made to mris_convert would
>> have to be applied to "label2surf" as well. I have noticed some
>> changes in the gifti files with your new mris_convert command.
>> However, I'm not so familiar with the gifti file structure.
>>
>> Maybe I could ask you to have a look into this?
>>
>> Also, If there is a easier way to achieve my goal any advise is welcome!
>>
>> Again, many thanks for your efforts so far!
>> Bastian.
>>
>>
>>
>>
>>
>>
>> On 29 May 2014 02:05, Nick Schmansky, MGH  wrote:
>>> Bastian,
>>>
>>> Hi, I've posted a new mris_convert which should solve the problem for
>>> you.  It's built for Centos 6, so if you need it for another platform,
>>> let me know.  It's here:
>>>
>>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
>>>
>>> Nick
>>>
>>>
>>>
>>> On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote:
>>>> Dear Freesurfer-Experts,
>>>>
>>>> I would like to create gifti-surfaces to use in matlab.
>>>>
>>>> That's what I am doing so far (latest FS-Version):
>>>>
>>>> mris_convert lh.white lh.white.gii
>>>>
>>>> I then try to open it using the "gifti" command (g=gifti('file.gii'))
>>>> (http://www.artefact.tk/software/matlab/gifti/)
>>>>
>>>> however, I get an error message from matlab:
>>>>
>>>>>>>>>>>>>>>
>>>> ??? Attempt to reference field of non-structure array.
>>>> Error in ==> gifti.subsref at 28
>>>> varargout{1} = this.data{j}.space.MatrixData;
>>>> Error in ==> gifti.struct at 17
>>>> [values{i,:}] = subsref(this(:), substruct('.',names{i}));
>>>> Error in ==> gifti.display at 17
>>>> eval([display_name ' = struct(this);']);
>>>>>>>>>>>>>>>>>>>
>>>>
>>>> Am I missing something? Is there anything special with the .gii file form 
>>>> FS?
>>>>
>>>> here is the surface file I created with mris_convert: 
>>>> http://we.tl/B2n4Ex6ifJ
>>>>
>>>> I am able to open the gifti file with freeview.
>>>> I also updated the gifti-toolbox in matlab to the latest version.
>>>>
>>>>
>>>> Any help is appreciated!
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>
>>>
>>> ___
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>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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Re: [Freesurfer] Freesurfer gifti-Surface in Matlab

[Bastian Cheng]

Hi Nick,

That works PERFECTLY! Thank you so much, it has been a big help!

I hope I may ask you another question:

I am actually trying to convert each freesurfer-label (from
aparc.annot) into separate surfaces (not gifti-labels)

So ideally I would convert lh.precentral.label > lh.precentral.gii.

I have used the command "label2surf", Part of FSL (build 504). (and I
have used the "new" gifti lh.white created with your updated version
as the input surface)

However, the output gifti does not open in matlab (instead shows the
same error message seen before).

Now I would guess that whatever changes you made to mris_convert would
have to be applied to "label2surf" as well. I have noticed some
changes in the gifti files with your new mris_convert command.
However, I'm not so familiar with the gifti file structure.

Maybe I could ask you to have a look into this?

Also, If there is a easier way to achieve my goal any advise is welcome!

Again, many thanks for your efforts so far!
Bastian.






On 29 May 2014 02:05, Nick Schmansky, MGH  wrote:
> Bastian,
>
> Hi, I've posted a new mris_convert which should solve the problem for
> you.  It's built for Centos 6, so if you need it for another platform,
> let me know.  It's here:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
>
> Nick
>
>
>
> On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote:
>> Dear Freesurfer-Experts,
>>
>> I would like to create gifti-surfaces to use in matlab.
>>
>> That's what I am doing so far (latest FS-Version):
>>
>> mris_convert lh.white lh.white.gii
>>
>> I then try to open it using the "gifti" command (g=gifti('file.gii'))
>> (http://www.artefact.tk/software/matlab/gifti/)
>>
>> however, I get an error message from matlab:
>>
>> >>>>>>>>>>>
>> ??? Attempt to reference field of non-structure array.
>> Error in ==> gifti.subsref at 28
>> varargout{1} = this.data{j}.space.MatrixData;
>> Error in ==> gifti.struct at 17
>> [values{i,:}] = subsref(this(:), substruct('.',names{i}));
>> Error in ==> gifti.display at 17
>> eval([display_name ' = struct(this);']);
>> >>>>>>>>>>>>>>>
>>
>> Am I missing something? Is there anything special with the .gii file form FS?
>>
>> here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ
>>
>> I am able to open the gifti file with freeview.
>> I also updated the gifti-toolbox in matlab to the latest version.
>>
>>
>> Any help is appreciated!
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
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[Freesurfer] Freesurfer gifti-Surface in Matlab

[Bastian Cheng]

Dear Freesurfer-Experts,

I would like to create gifti-surfaces to use in matlab.

That's what I am doing so far (latest FS-Version):

mris_convert lh.white lh.white.gii

I then try to open it using the "gifti" command (g=gifti('file.gii'))
(http://www.artefact.tk/software/matlab/gifti/)

however, I get an error message from matlab:

>>>
??? Attempt to reference field of non-structure array.
Error in ==> gifti.subsref at 28
varargout{1} = this.data{j}.space.MatrixData;
Error in ==> gifti.struct at 17
[values{i,:}] = subsref(this(:), substruct('.',names{i}));
Error in ==> gifti.display at 17
eval([display_name ' = struct(this);']);
>>>

Am I missing something? Is there anything special with the .gii file form FS?

here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ

I am able to open the gifti file with freeview.
I also updated the gifti-toolbox in matlab to the latest version.


Any help is appreciated!
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[Freesurfer] Create gifti surfaces from lh.white for MATLAB

[Bastian Cheng]

Dear Freesurfer-Experts,

I would like to create gifti-surfaces to use in matlab.

That's what I am doing so far:

mris_convert lh.white lh.white.gii

I then try to open it using the "gifti" command
(http://www.artefact.tk/software/matlab/gifti/)

however, I get an error message from matlab:

>>>
??? Attempt to reference field of non-structure array.

Error in ==> gifti.subsref at 28
varargout{1} = this.data{j}.space.MatrixData;

Error in ==> gifti.struct at 17
[values{i,:}] = subsref(this(:), substruct('.',names{i}));

Error in ==> gifti.display at 17
eval([display_name ' = struct(this);']);
>>>

Am I missing something? Is there anything special with the .gii file form FS?

Any help is appreciated!
Bastian
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[Freesurfer] longitudinal stream percentage change

[Bastian Cheng]

Dear freesurfer-experts,

I have successfully done a longitudinal analysis on cortical thickness
changes over 2 timepoints (0 and 1 year).

My question is:

If I look at the -individual- overlays of perc. change (i.e. pc1fit),
only positive values are shown.
whereas at the -fsaverage- view, positve AND negative values are shown
(i.e. thinning and thickening)

I understood that long_mris_slopes calculates the "percent thinning per year".
But is there a way to show both sides of the histogramm (i.e. from -2
to +2) also on the -individual- overlay?

This might be a naive question, however, any help is greatly appreciated!

Bastian.
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