Re: [Freesurfer] aparcstats2table

[Devika K]

External Email - Use Caution

Hi,

Can I use the below command to extract the cortical thickness using
Destrieux Atlas from longitudinally preprocessed subjects?

aparcstats2table --hemi lh \
  --subjects 004 021 040 067 080 092 \
  --meas thickness \
  --parc aparc.a2009s \
  --tablefile lh.aparc.a2009.thickness.table

Regards
Devika K
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Re: [Freesurfer] Cannot allocate memory

[Gabriel Tapia]

External Email - Use Caution

Hello Bruce thank you for your quick reply,
Where should I look to get all these files?
The idea to check them is to confirm that the MRI went wrong at some point,
right?
Thanks,

Gabriel Tapia 
www.Partage3D.fr 
+33 6 62 90 11 67


Le mar. 25 févr. 2020 à 04:09, Bruce Fischl  a
écrit :

> Hi Gabriel,
>
> that is a huge defect and generally means something major has gone wrong.
> Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix
> over the wm.mgz file to see what is wrong (usually something like a big
> chunk of skull is left over and connected to the surface, sometimes
> through orbital fat in the eye sockets)
>
> If you can't sort it out let us know and we will help
> cheers
> Bruce
>
> On Tue, 25 Feb 2020, Gabriel Tapia
> wrote:
>
> >
> > External Email - Use Caution
> >
> > Hello dear Freesurfer developers, nice to e-meet you and thank you for
> > working on this open source software!
> >
> > I am trying to produce a 3D file of a brain.
> > The command I am trying to run is recon-all and here is the error I get:
> > CORRECTING DEFECT 57 (vertices=33394, convex hull=9966)
> > Excessive topologic defect encountered: could not allocate 140742253
> > edges for retessellation
> > Cannot allocate memory
> >
> > The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0
> > The platform is Red Hat 64-bit running in a Virtual box with 7835mb
> > allocated memory.
> > You will find the corresponding log file attached.
> >
> > Isn't it surprising that I don't have enough memory with 7835mb
> allocated?
> > Sorry, I am new to Freesurfer and there might be something I didn't get.
> > Thank you very much in advance for your help,
> > Regards,
> >
> > Gabriel Tapia
> > www.Partage3D.fr
> > +33 6 62 90 11 67
> >
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Re: [Freesurfer] Cannot allocate memory

[Bruce Fischl]

Hi Gabriel,

that is a huge defect and generally means something major has gone wrong. 
Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix 
over the wm.mgz file to see what is wrong (usually something like a big 
chunk of skull is left over and connected to the surface, sometimes 
through orbital fat in the eye sockets)


If you can't sort it out let us know and we will help
cheers
Bruce

On Tue, 25 Feb 2020, Gabriel Tapia 
wrote:




External Email - Use Caution

Hello dear Freesurfer developers, nice to e-meet you and thank you for
working on this open source software!

I am trying to produce a 3D file of a brain.
The command I am trying to run is recon-all and here is the error I get:
CORRECTING DEFECT 57 (vertices=33394, convex hull=9966)
Excessive topologic defect encountered: could not allocate 140742253
edges for retessellation
Cannot allocate memory

The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0
The platform is Red Hat 64-bit running in a Virtual box with 7835mb
allocated memory.
You will find the corresponding log file attached.

Isn't it surprising that I don't have enough memory with 7835mb allocated?
Sorry, I am new to Freesurfer and there might be something I didn't get.
Thank you very much in advance for your help,
Regards,

Gabriel Tapia
www.Partage3D.fr
+33 6 62 90 11 67

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[Freesurfer] Cannot allocate memory

[Gabriel Tapia]

External Email - Use Caution

Hello dear Freesurfer developers, nice to e-meet you and thank you for
working on this open source software!

I am trying to produce a 3D file of a brain.
The command I am trying to run is recon-all and here is the error I get:



*CORRECTING DEFECT 57 (vertices=33394, convex hull=9966) Excessive
topologic defect encountered: could not allocate 140742253 edges for
retessellation Cannot allocate memory*

The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0
The platform is Red Hat 64-bit running in a Virtual box with 7835mb
allocated memory.
You will find the corresponding log file attached.

Isn't it surprising that I don't have enough memory with 7835mb allocated?
Sorry, I am new to Freesurfer and there might be something I didn't get.
Thank you very much in advance for your help,
Regards,

Gabriel Tapia 
www.Partage3D.fr 
+33 6 62 90 11 67
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Re: [Freesurfer] Which FDG-PET file to use for PETSufer?

[Kate Marvel]

External Email - Use Caution

Thank you very much Douglas for the information.

Kate

On Mon, Feb 24, 2020 at 2:44 PM Douglas N. Greve 
wrote:

> what are those three? The same data just oriented in a differeent way? If
> so, then it does not matter as long as the orientation info is correct.
> Load one into freeview to assure that the cor view actually shows up as
> cor, etc. One thing you will not be able to check is whether there is a
> left-right flip
>
> On 2/24/2020 3:30 PM, Kate Marvel wrote:
>
> External Email - Use Caution
> Hi FreeSurfer Users,
>
> I would like to perform PET analysis using PETSurfer and I have the
> following FDG-PET NIfTI files below:
>
> 1. TRANSAXIAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii
>
> 2. SAGITTAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii
>
> 3. CORONAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii
>
> Which of the 3 NIfTI files above should one use for the PETSurfer?
>
> Thank you.
>
> --
> kate
>
> ___
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>
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Re: [Freesurfer] Which FDG-PET file to use for PETSufer?

[Douglas N. Greve]

what are those three? The same data just oriented in a differeent way? 
If so, then it does not matter as long as the orientation info is 
correct. Load one into freeview to assure that the cor view actually 
shows up as cor, etc. One thing you will not be able to check is whether 
there is a left-right flip


On 2/24/2020 3:30 PM, Kate Marvel wrote:


External Email - Use Caution

Hi FreeSurfer Users,

I would like to perform PET analysis using PETSurfer and I have the 
following FDG-PET NIfTI files below:


1. TRANSAXIAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii

2. SAGITTAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii

3. CORONAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii

Which of the 3 NIfTI files above should one use for the PETSurfer?

Thank you.

--
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Re: [Freesurfer] samseg permissions error

[Hoopes, Andrew]

Hi Andrew,

Thanks for pointing this out, it looks like the permissions of our fsaverage 
subjects have all changed since yesterday! Will fix this now

Best,
Andrew


From:  on behalf of "Russo, Andrew 
William" 
Reply-To: FS Help 
Date: Monday, February 24, 2020 at 10:51 AM
To: FS Help 
Subject: [Freesurfer] samseg permissions error

Hello Freesurfer Developers,

I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do 
not have permission to access the directory 
/usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory?

ValueError: file /usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does 
not exist
ERROR: fs_time run_samseg

I did not find any related issues with samseg on the archive and I have had it 
work in the past. Before running samseg I sourced the freesurfer environment:
export FREESURFER_HOME=/usr/local/freesurfer/dev
source $FREESURFER_HOME/SetUpFreeSurfer.sh
(Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)

Thank you in advance,
Andrew

Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531

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[Freesurfer] Which FDG-PET file to use for PETSufer?

[Kate Marvel]

External Email - Use Caution

Hi FreeSurfer Users,

I would like to perform PET analysis using PETSurfer and I have the
following FDG-PET NIfTI files below:

1. TRANSAXIAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii

2. SAGITTAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii

3. CORONAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii

Which of the 3 NIfTI files above should one use for the PETSurfer?

Thank you.

-- 
kate
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[Freesurfer] Pre-release (beta) version of FreeSurfer v7 now available

[Douglas N. Greve]

You can now download and install the beta version 7 of FreeSurfer. See 
this page

https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1

The purpose of this beta is for users to install and run FreeSurfer 
 on some of their 
data sets using their computers and their commands and their 
post-processing to help us track down any errors prior to the full 
release scheduled for mid March. To that end, we would like for you to 
do several tests on a couple of subjects:


 * Do not use the beta version for any analyses that you want to
   publish. Only use full releases.
 * Run recon-all on the various computers (desktops, clusters, etc)
   that you use
 * Run recon-all with any special flags that you might use (eg, expert
   options)
 * Edit the recon and verify that the changes are taken and preserved
 * Run recon-all on problem data sets
 * Run recon-all on hires data (just add -hires flag), where hires is
   voxel size less than 1mm
 * Run recon-all with T2 or FLAIR input (1mm or hires)
 * Run longitudinal recon-all
 * Run the subfield analysis (hippcampal subfields, amygdalar and
   thalamic nuclei). You can do this by just adding -subfields to
   recon-all
 * Run samseg on a data set. We'll have more docs on samseg later, but
   for now SAMSEG = Sequence Adaptive Multimodal Segmentation can take
   any modality (or combination) and produce a volume segmentation
   (seg.mgz, like the aseg.mgz) -- it does not replace recon-all
   (samseg does not create surfaces, only volumetric segmentation). You
   can run it with something like "samseg --i inputvolume.mgz --o
   samsegdir". It should take about 45min. For now, we just want to
   make sure that it runs on your system.
 * Run any special post-processing to make sure that nothing breaks.

We'll update the release notes with new features for the full release, 
but for now you should know that some features are not present in v7 
(QDEC, GPU-capability, and recon-all -make). A new version of Tracula is 
in the works but probably will not be out until April or so; we'll have 
a minor release when it is ready.


Let us know how it goes!
The FreeSurfer Team


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[Freesurfer] Registration error

[Harrigan, Timothy P.]

External Email - Use Caution

Hi,
I'm trying to learn to use Freesurfer to see if I can use it for some academic 
work on TBI.  I downloaded it to a spare laptop at home, and filled out the 
registration form, and I got a message that stated "Registration Error:  
Spammer. Go Away."

How could I address this?
Thanks
Tim

Timothy P. Harrigan ScD
Research and Exploratory Development Division
Johns Hopkins University Applied Physics Laboratory
Phone: 240-228-5943
Cell/Text: 240-280-9444

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[Freesurfer] samseg permissions error

[Russo, Andrew William]

Hello Freesurfer Developers,

I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do 
not have permission to access the directory 
/usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory?

ValueError: file /usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does 
not exist
ERROR: fs_time run_samseg

I did not find any related issues with samseg on the archive and I have had it 
work in the past. Before running samseg I sourced the freesurfer environment:
export FREESURFER_HOME=/usr/local/freesurfer/dev
source $FREESURFER_HOME/SetUpFreeSurfer.sh
(Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)

Thank you in advance,
Andrew

Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531


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Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

[Kate Marvel]

External Email - Use Caution

Hi Bruce,

Thank you very much Bruce.

Kate

On Mon, Feb 24, 2020 at 8:50 AM Bruce Fischl 
wrote:

> Hi Kate
>
> the .lta format is for a linear registration (in ascii). YOu can just cat
> it to see the contents - it is not a PET image (which will be stored in
> .mgz or .nii). mri_convert or mri_vol2vol can be used to apply the
> registration and/or change the output format (if you specify file.nii or
> file.nii.gz it will write in Nifti)
>
> cheers
> Bruce
>
>
> On Mon, 24 Feb 2020, Kate Marvel wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Douglas,
> > Is there a way to save the registered PET image in NIfTi format instead
> of
> > .lta?
> >
> > Kate
> >
> > On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve  >
> > wrote:
> >   Not sure what you are trying to do. An lta file is a matrix and
> >   nifti is a format for storing images.
> >
> >   On 2/21/2020 7:52 AM, Kate Marvel wrote:
> >
> >   External Email - Use Caution
> >
> >   Hi All,
> > How do you convert the registered file (.lta) into NIfTI format
> > in PETsurfer.
> >
> > Thanks,
> >
> >
> > ___
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> >
> >
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> >
> >
> >
> > --
> > kate
> >
> >___
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-- 
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[Freesurfer] skull stripping problem

[Marina Fernández]

External Email - Use Caution

Dear Freesurfeer experts,

After running the recon-all, a part of the temporal lobe of one subject was
removed.

I used the watershed algorithm to be less agressive in the skull stripping
step:

recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001

And the problem was solved in the brainmask.mgz volume because I can see
the temporal lobe completely, but the surfaces are still displaced. In
order to correct the surfaces I used the white matter edit tool but there
is no change after correcting WM and running the recon-all -autorecon2-wm
-autorecon3. I also used control points and but the following error was
shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3:

recon-all -s sub_001 existed with errors

I detected that there are very high values in the white matter of this part
of the temporal lobe (even 132), maybe it has something to do. What can I
do to solve the problem with this subject?


Thank you very much in advance.

Best regards,

Marina.
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Re: [Freesurfer] Apply transformation

[Adam Rytina]

External Email - Use Caution

Hello all,

is it possible to transform a binary mask (a transformation matrix 4x4 acquired 
by registration of an anatomical and a diffusion image) and change a final FOV 
by specifying a diffusion reference image? Or the transform can be applied only 
on structural image?

I am still struggling with the transformation of my binary mask as explained 
below.

Thanks a lot
Regards
Adam


Od: Adam Rytina 
Odesláno: středa 19. února 2020 8:11
Komu: Greve, Douglas N.,Ph.D. 
Předmět: Fw: [Freesurfer] Apply transformation

Hello,

please, could you help me with this case? What am I doing wrong?

Thanks a lot


Od: freesurfer-boun...@nmr.mgh.harvard.edu 
 za uživatele Adam Rytina 

Odesláno: sobota 15. února 2020 19:52
Komu: Freesurfer support list 
Předmět: Re: [Freesurfer] Apply transformation


External Email - Use Caution

Thanks, unfortunately, I am making some mistake but I don´t know where.

First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is 
saved in /usr/local/freesurfer/subjects/anatomical).
Then in the /usr/local/freesurfer/data I run mri_robust register command of the 
T1 and diffusion DWI data. The registration.lta file is saved here.

Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder 
/usr/local/freesurfer/data that I want to transform to the anatomical T1 space.

In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta 
registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical 
--fstarg"

To sum up, I am aiming to apply a transformation matrix on the T1 anatomical 
brain mask and transform it to the T1 space defined by 3D T1 image.
The problem is this command transforms orig.mgz file (a skull stripped T1 
image) instead of 3D_T1_brain_mask.nii.

Please, do you know where I make mistake?

Thanks a lot

Od: freesurfer-boun...@nmr.mgh.harvard.edu 
 za uživatele Douglas Greve 

Odesláno: sobota 15. února 2020 17:15
Komu: freesurfer@nmr.mgh.harvard.edu 
Předmět: Re: [Freesurfer] Apply transformation

Yes, mri_vol2vol

On 2/15/20 11:07 AM, Adam Rytina wrote:

External Email - Use Caution

Hello all,

I want to apply the saved transformation (a transformation matrix 4x4 acquired 
by registration of an anatomical and a diffusion image) on my input anatomical 
mask and change a final FOV by specifying a diffusion reference image (its 
voxels size). It means to apply the same command as the command ApplyXFM in FSL 
FLIRT. Does this option exist also in Freesurfer?

Thanks a lot
Regards
Adam




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Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

[Bruce Fischl]

Hi Kate

the .lta format is for a linear registration (in ascii). YOu can just cat 
it to see the contents - it is not a PET image (which will be stored in 
.mgz or .nii). mri_convert or mri_vol2vol can be used to apply the 
registration and/or change the output format (if you specify file.nii or 
file.nii.gz it will write in Nifti)


cheers
Bruce


On Mon, 24 Feb 2020, Kate Marvel wrote:



External Email - Use Caution

Hi Douglas,
Is there a way to save the registered PET image in NIfTi format instead of
.lta?

Kate

On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve 
wrote:
  Not sure what you are trying to do. An lta file is a matrix and
  nifti is a format for storing images.

  On 2/21/2020 7:52 AM, Kate Marvel wrote:

  External Email - Use Caution

  Hi All,
How do you convert the registered file (.lta) into NIfTI format
in PETsurfer.

Thanks,


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Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

[Kate Marvel]

External Email - Use Caution

Hi Douglas,

Is there a way to save the registered PET image in NIfTi format instead of
.lta?

Kate

On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve 
wrote:

> Not sure what you are trying to do. An lta file is a matrix and nifti is a
> format for storing images.
>
> On 2/21/2020 7:52 AM, Kate Marvel wrote:
>
> External Email - Use Caution
> Hi All,
>
> How do you convert the registered file (.lta) into NIfTI format in
> PETsurfer.
>
> Thanks,
>
>
> ___
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>
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Re: [Freesurfer] cluster size threshold

[Douglas N. Greve]

You need to find the correct CDF file, eg, if the final FWHM is 12, it 
would be in
$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm12/abs/th30/mc-z.cdf 


To get the FWHM look in glmdir/fwhm.dat and round down
in the mc-z.cdf file, find the row where the MaxClustCDF drops below 
.05/2=.025, then look at the MaxClustBin for the critical cluster size


On 2/24/2020 6:49 AM, Elisa Castaldi wrote:


External Email - Use Caution

Dear experts,

To perform a Monte Carlo based cluster correction, I have run the 
following line:


mri_glmfit-sim --glmdir glmdir --mczsim 3 abs --cwp 0.05 --2spaces 
--a2009s


I need to figure out which is the minimum number of voxels required 
for a cluster to be considered significant.
In other words, which is the cluster _size_ threshold in this case? 
Where can I find this information?


Thanks
Elisa

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Re: [Freesurfer] Version Beta 7.0

[Douglas N. Greve]

We have not released stable 7 yet. Technically we have not released 
7beta yet but only because I need to make the announcement and write up 
some docs.


On 2/24/2020 2:46 AM, Victor Montal Blancafort wrote:


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Freesurfer developers,
I have seen from the download webpage, that there is already a v7.0 
beta version.
Since we were planing to re-run a lot of individuals 1000+ with 
Freesurfer6, I was wondering if you could provide timings regarding 
the release of stabe 7.0.
Also, could you briefly explain the main changes in this version? We 
are mainly interested on cortical thickness analysis, so... there will 
be big differences in the recon-all pipeline?


Thank you in advance!
V.

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Re: [Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary

[Douglas N. Greve]

Try setting -max XXX
where XXX is the maximum allowable thickness. It is default to 5, so try 
something large


On 2/21/2020 11:36 AM, CiRong Liu wrote:


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Dear experts of the freesurfer,

I was trying to create the white matter and pial surfaces of 
the cerebellum of the marmoset, based on ultra-high (80um) resolution 
ex-vivo images.


I manually segment the cerebellum into the white matter and the gray 
matter and change the header information to 1mm.


Based on the manual segmented files, I created white matter surfaces 
(rh.orig).


I tried to use the mris_make_surfaces to expand the white matter to 
create the matched pial surface.


However, the /mris_make_surfaces/ failed to push the surface enough. 
See the attached files and screenshots.


I tried smoothing the segmentation, enhancing the contrasts, and 
tested different expert option (for example: -max_csf 0.1 
-min_gray_at_csf_border 1)


This was this best I got, but still cannot get an optimal result (not 
pushed enough):


/mris_mask_surfaces -max_csf 0.1 -min_gray_at_csf_border 1 -orig_wm 
orig -orig_pial orig -noaseg -noaparc -T1 ceb_sm marmosetceb rh /


Since I have already manually segmented the cerebellum, *is there a 
way to force the /mris_make_surfaces/ to expand to the boundary of the 
image?*


The files can be download to replicate what I did:
https://pitt.box.com/s/6269a9mnwbs6zi0azn08dn55u47yfa7i

Thank you very much!

Best Regards, CiRong Liu

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Re: [Freesurfer] Optseq2 help needed

[Douglas N. Greve]

By default, optseq2 assumes that you want to perform an FIR analysis 
where you get an average for each post-stimulus time point so that you 
can create a waveform. This is in contrast to assuming the shape to the 
hemodyn respnse where you only estimate a single value (the amplitude). 
By default, the time between FIR waveform points is the TR, but you can 
perform sub-TR estimation by setting the dPSD to less than the TR. The 
problem is that every estimate you make reduces the efficienecy. So, 
assuming a shape is more efficient than an FIR because it only has one 
estimate. An FIR with dPDS=TR is more efficient than dPSD=TR/2 because 
there are half as many estimates. Probably when you go to analyze the 
data you will use an assumed shape, and then you will get the efficiency 
back.


On 2/21/2020 9:43 AM, Gergely Darnai wrote:


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Dear Developers,

I am planning to run PVT (psychomotor vigilance task) in fMRI using 
event related design. This is an extremely simple reaction time task: 
participant has to respond to the appeared geometric shape as quickly 
as possible. The key feature of this paradigm is that we will have 
fluctuating and quite rapid event presentation times (ranging between 
300 and 500 msec). Another important information is that we will use 
FSL FEAT for the evaluation. We decided to use opseq2 to optimize the 
design with the following parameters:


optseq2 --ntp 150 --tr 2 --psdwin 0 20 --ev evt1 1 45 --nkeep 3 --o 
exp --nsearch 1 --tnullmin 3 --tnullmax 11 --repvar 10


Although with this design I get quite satisfying efficiency and VRF 
scores I do not understand that if I decrease dPSD why does it have 
significant negative effect on efficiency and VRF. Could you explain 
this? If I understand well, this is the only option to shift the onset 
of the event from the scanning points, and I would assume that if 
there is fluctuation in time between scanning points and stimuli 
presentation, it would help to "catch" the hemodynamic response easier 
(if the stimulus onset always goes together with the scans, we can 
always catch the same timepoints of the HRF). Did I misunderstand 
something? If I use FSL that is based on HRF estimation (and not on 
FIR), do these parameters (dPSD) and scores (efficiency & VRF) have 
meaning and function at all? My last question is related to event 
duration. Although I have fluctuating and short events, as you can see 
I chose 1 sec (because it has to be the integer multiple of the dPSD). 
Is it problematic?


Thank you for your suggestions,

Gergely

-
Gergely Darnai PhD
Department of Behavioural Sciences
Medical School, University of Pécs
Phone: +36/72/536-256
Fax: +36/72/536-257
H-7624 Szigeti u. 12, Pécs, Hungary

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Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

[Douglas N. Greve]

Not sure what you are trying to do. An lta file is a matrix and nifti is 
a format for storing images.


On 2/21/2020 7:52 AM, Kate Marvel wrote:


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Hi All,

How do you convert the registered file (.lta) into NIfTI format in 
PETsurfer.


Thanks,


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Re: [Freesurfer] surfreg function

[Douglas N. Greve]

it is ok to spec -surfreg, but is not necessary in this case 
mris_preproc will change the name when you spec a target subject 
(eventhough the says that the default is sphere.reg)


On 2/21/2020 6:20 AM, Marina Fernández wrote:


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Hi Doug,

Thank you for your replay.

I understood that if I did not specify "--surfreg 
my_avg_subject.sphere.reg"  mri_preproc was going to use the original 
file (sphere.reg), because in the help of mri_preproc it mentions this:


--surfreg SurfReg : default is sphere.reg

With this in mind,do you think it would not be necessary to specify it 
in mris_preproc?


What is the difference between sphere.reg and my_avg_subject.sphere.reg?

Best wishes,
Marina


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Re: [Freesurfer] GLM DOSS questions

[Douglas N. Greve]

On 2/21/2020 4:01 AM, Ferraro, Pilar wrote:


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Dear Freesurfer experts,

I’ve just completed a GLM analysis in Freesurfer and I’d like to be 
sure that all the steps I’ve performed are the right ones.


My analysis is looking at age related changes in cortical thickness in 
one group of patients, after regressing out the effects of disease 
duration. I obviously assume an inverse relationship between age and 
cortical thickness so that older age would be associated with cortical 
thickness reductions in specific brain regions.


To test this hypothesis with Freesurfer I’ve used a GLM DOSS design.
I’ve generated a fsgd file with the first column being the list of 
patients, the second column the age of patients, and the third column 
the disease duration.

Then I’ve run the mris_preproc command.

Afterward,  I’ve generated 2 contrast matrices (one for the left and 
one for the right hemisphere) with the following structure: 0 -1 0.


1 question. Is the contrast matrices structure I’ve chosen the most 
appropriate one for the hypothesis I’d like to test?
Yes, but if you are going to use -1, you need to keep track of that when 
you specify the sign (but you are using abs so it does not matter). 
Also, you don't need different fsgd and contrast files for each hemisphere.


Then, I’ve run the glm analysis using the mri_glmfit command.

To visualize the results I’ve used the freeview -f command and set the 
overlay_threshold to 1,5 instead of 4, cause I was interested in 
looking at all results significant at p < 0.05.


2 question. Is the overlay_threshold I’ve used the correct one?
for visualization, you can use whatever threshold you want. But if you 
are going to use monte carlo simulations, then you need p<.001. If you 
want to keep p<.05, then you have to do permutation.


Lastly, I was interested in looking at my results after Montecarlo 
correction, so I’ve run the simulation using the mri_glmfit-sim command.

However, here I’ve changed few options:

mri_glmfit-sim \
  --glmdir lh.dur.glmdir \
  --cache 4 neg \ (here I’ve changed to 1,5 since I was interested 
again at a P value < 0,05 and not < 0.0001 and I’ve changed the neg 
option with abs since I was interested in absolute values identified 
through the previously run analysis)

  --cwp  0.05\
  --2spaces

3 question. Are the edits I made to the command correct? It is not 
perfectly clear to me which one should be the preferred sign for the 
analysis (neg, pos or abs?).
abs is an unsigned test. If you have an aprior hypothesis, then you can 
set the sign to that. Eg, if you are expecting the age slope to be 
negative, then you could choose negative (or in your case positive since 
you flipped the sign in the contrast)


In the end, in order to visualize the Montecarlo corrected results 
I’ve used again the Freeview -f command and again I’ve sent the 
overlay threshold to 1,5 since I was interested in all significant 
clusters at P < 0,05.


4 question. Again, this threshold is the correct one for my purpose?

It will show all the clusters that are at p<.05 corrected.


I have one last question concerning the Montecarlo simulation. Are 
there any cases in which you would suggest to do not use it since it 
would not be an appropriate correction?
I'm recommending that everyone use permutation at this point. MC can 
generate inlfated false positives


Sorry for the long email but I needed to report all the steps in order 
to get an answer.

Many thanks for all the help you’ll be able to provide.

Best,

Pilar Ferraro

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Re: [Freesurfer] Extract specific LGI and Volume values

[Douglas N. Greve]

Try using freeview

On 2/18/2020 8:17 PM, Tien Pham wrote:


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Thank you for your email.
I tried to load the label with qdec and freeview and both were not worked.
When i tried with qdec, It said '' load the surface first '' then I 
did but It did not work and showed some errors.
The other way when I tried to load with qdec, qdec was closed suddenly 
without any notification.

I am looking forward to hearing from you.

On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


What tool are you trying to use to load the label? What happens
when you try?

On 2/7/2020 10:11 PM, Tien Pham wrote:


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Thank you for your email. I run exactly the command
mri_label2label as you suggested, and the command finished
without any problem.
But I did not know why I could not open the label.
Please help me. Thank you once again.

On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

sorry for the delay. You will have to use mri_label2label to
map the label from the fsaverage space to the individual space


On 1/31/2020 10:01 PM, Tien Pham wrote:


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Can you read my message?
I used longitudinal pipeline for my data set with two time
points and measured the LGI differences between them.
Then I created the label based on significant clusters which
showed in QDEC.
I tried to load the label on the subjects in cross, base,
long steps but it did not work.
I am looking forward to hearing from you. Thank you very much.

On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Sorry, I do not have the previous emails, can you repost
with previous emails in the message?

On 1/28/2020 7:35 PM, Tien Pham wrote:


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Thank you for your response.
I used longitudinal pipeline for my data set with two
time points and calculated the LGI differences between
them.
Then I created the label based on significant clusters
which showed in QDEC.
I tried to load the label on subjects in cross, base,
long steps but it did not work.
I am looking forward to hearing from you. Thank you so
much.

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[Freesurfer] cluster size threshold

[Elisa Castaldi]

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 Dear experts,

To perform a Monte Carlo based cluster correction, I have run the following
line:

mri_glmfit-sim --glmdir glmdir --mczsim 3 abs --cwp 0.05 --2spaces --a2009s

I need to figure out which is the minimum number of voxels required for a
cluster to be considered significant.
In other words, which is the cluster *size* threshold in this case? Where
can I find this information?

Thanks
Elisa
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