[Freesurfer] Multiple Comparison Question for surface-based analyses

[Ajay Kurani]

Hello Freesurfer Experts,
   Recently there were two article published regarding clusterwise
simulations for volumetric fmri analyses and potential errors for
underestimating clusterwise extent thresholds.

1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
2) biorxiv.org/content/early/2016/07/26/065862

One issue pointed out from these articles seems software specific, however
the second issue is determining the proper clustersize.  The heavy-tail
nature of spatial smoothness seems to be ignored and a gaussian shape is
generally assumed, leading to an underestimation of the spatial smoothness
which can affect cluster size calculations.  The issues are highlighted in
the second article above.

I created my own monte carlo simulation in Freesurfer for a specific brain
template and I wanted to find out if these concerns also apply to my
surface based simulations?  I am not sure if it does since the monte carlo
tool is a GRF simulation as opposed to an analytic equation, however given
that these articles were highlighted very recently, I wanted to ensure I am
running things appropriately for surface based cortical thickness/dti
analyses.

Thanks,
Ajay
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Re: [Freesurfer] group analysis/ region of interest (ROI) approach

[miracle ozzoude]

Thanks doug. Also, Please can you verify if this are the right codes for
performing ROI surface based analysis using the command line. I tried to
reverse the whole brain analysis tutorial with some of the previous threads
i read. I'm trying to mask the entorhinal and MT and then perform ROI on
them using GLM. Thanks a lot

CREATE MASK USING MRI_BINARIZE
setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri
cd users/paul/desktop/ims/fsaverage/mri
mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz

MERGE TO LABELS
cd users/paul/desktop/ims/fsaverage/label
mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label

MRIS_PREPROC
cd users/paul/desktop/ims
mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas
thickness --out lh.filename.thickness.00.mgh

MRI_SURF2SURF
mri_surf2surf --hemi lh --s fsaverage --sval lh.filename.thickness.00.mgh
--fwhm 10 --label-trg fsaverage/label/lh.2mask.label --tval
lh.filename.thickness.10B.mgh

GLM
mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods --C
contrastmatrix.mtx --surf fsaverage lh --label
fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir

CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations
mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 mc-z.positive
--sim-sign pos --cwpvalthresh 0.05 --2spaces

On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve 
wrote:

> I think there is an example on the wiki in the ROI analysis section.  See
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
>
> After you run aparcstats2table, you can run mri_glmfit with --table
> aparcstatstable instead of --y. The output folder will have tables with
> lists of ROIs and p-values
>
>
>
> On 7/30/16 5:33 PM, miracle ozzoude wrote:
>
> Hey FreeSurfer experts,
> Does anyone know the steps i have to perform if I want to conduct surface
> based thickness analysis using GLM but with ROI approach. Thank you very
> much.
> Best,
> Paul
>
>
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Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR

[Douglas Greve]

That recon-all command will not work as the FLAIR input should be a 
simple FLAIR image. The FLAIR will only correct the pial surface and 
will have nothing to do with lesion segmentation. Emily Lindermer has a 
tool that can take a T1 and FLAIR and produce a lesion map; but given 
that you already have manual segmentations, maybe that is not so 
helpful. One thing you can do is to edit the aseg.mgz to insert your 
lesions. First run recon-all with -autorecon1 -autorecon2 instead of 
-all. Then, in matlab,



aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg

manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever 
format, but should be binary


ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0);

newaseg = aseg;

newaseg.vol(ind) = 77;

MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so 
make a backup



Then run recon-all with -autorecon2-cp -autorecon3



On 8/1/16 7:35 AM, Silas wrote:



Dear FreeSurfer team,


I'm doing a structural analysis with 50 MS patients and 50 healthy 
controls (T1, T2 and FLAIR). The MS patients have multiple lesions 
mainly in white matter. My co-worker did manual editing (bullet 
points) in the FLAIR images, and i would like to use these edits when 
running recon-all in order to avoid further manual editing.



The data i'm working with is already resliced to 1 mm and 
co-registered in MNI-space.


1) Can i use this data or would it be preferable to use the original T1's?


My thought was to run the following command:

recon-all -subject subjectname -i /path/to/input_volume -FLAIR 
/path/to/FLAIR_volume_with_edits-FLAIRpial  -all
2) Does this look correct? Is there anything i should be aware of? -> 
update: Does this command only improve the pial surface? How can i 
also improve the white mater segmentation (white) using FLAIR 
corrections?


3) Does it make a difference running recon-all -all with the FLAIR 
image - compared to running recon-all -autorecon3 with the FLAIR after 
running recon-all -all with only the T1?


4) I've also thought about using the lesion segmentation toolbox for 
SPM and completely avoid manual editing - is this preferable to using 
the FLAIR with manual editing?


5) How is the general strength of analysing corpus callosum 
structurally in MS patients using FreeSurfer?



Best, Silas



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Re: [Freesurfer] brain mask and T1 are not the same size

[Isabelle Deschamps]

So you're saying that the dimension changed after you ran freeview and 
saved the volume? Can you replicate it? ie, if you make a copy of the 
brainmask.mgz, then edit the copy, does it do the same thing every time 
you make a copy and edit it?



Yes it does. I tried multiple time your suggestion (copying brain mask) and the same error happens. I tried erasing different brain areas of the brain mask
 to understand the source of the problem, and for these 4 participants it does not seem to matter what I erase or not. The dimensions change.



Thank you for your help,



Isabelle

Isabelle

On Jul 30, 2016, at 11:23 AM, "freesurfer-requ...@nmr.mgh.harvard.edu"  wrote:



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Today's Topics:

  1. Fwd: question about volume of mask (Dorsa Haji Ghaffari)
  2. brain mask and T1 are not the same size (Isabelle Deschamps)
  3. Re: error during longitudinal -long stream (Jinsong Tang)
  4. Research Assistants needed for longitudinal brain development
 study at Boston Children's Hospital (Gaab, Nadine)
  5. Re: error during longitudinal -long stream (Martin Reuter)
  6. MNI coordinates of all the vertices of fsaverage (Sabin Khadka)
  7. Running Retinotopy in FSFAST,    Design Matrix has Empty
 Regressors (Taylor, Johnmark)
  8. mri_normalize, 110 is too dark (tvg[fs])
  9. Re: brain mask and T1 are not the same size (Douglas Greve)
 10. Re: mri_normalize, 110 is too dark (Bruce Fischl)
 11. Where are time series from adjusted (post selxavg3)    ROIs
 (ERIK JAHNER)
 12. Re: significance overlay in freeview (Caroline Beelen)
 13. Running recon-all with T1 and FLAIR (Silas)
 14. Re: error during longitudinal -long stream (Jinsong Tang)


--

Message: 1
Date: Fri, 29 Jul 2016 12:08:43 -0400
From: Dorsa Haji Ghaffari 
Subject: [Freesurfer] Fwd: question about volume of mask
To: Freesurfer support list 
Message-ID:
   
Content-Type: text/plain; charset="utf-8"

Hi Bruce,

I was able to reslice the thalamus mask correctly, but when I measure the
volume of the resliced thalamus, is not the same as the original thalamus.
I was wondering why that is happening and which volume is more accurate. I
appreciate any suggestions. I have attached both masks. Also can you tell
me how to measure the volume of the resliced thalamus in Freesurfer?

Thank you

Dorsa
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Message: 2
Date: Fri, 29 Jul 2016 16:09:31 +
From: Isabelle Deschamps 
Subject: [Freesurfer] brain mask and T1 are not the same size
To: "freesurfer@nmr.mgh.harvard.edu" 
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Message: 3
Date: Fri, 29 Jul 2016 09:26:58 -0700
From: Jinsong Tang 
Subject: Re: [Freesurfer] error during longitudinal -long stream
To: Freesurfer support list 
Message-ID:
   
Content-Type: text/plain; charset="utf-8"

Hi Martin,

I checked all data are completed except the link to  fsaverage,
lh.EC_average and rh.EC_average.   I run one analysis from the terminal. it
works. if I run multiple analysis at the same time, it failed.
When I manually linked the 3 files, then run multiple analysis at the same
time, it works good.

Best,

Jinsong

O

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

[Douglas Greve]

I think there is an example on the wiki in the ROI analysis section.  See

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

After you run aparcstats2table, you can run mri_glmfit with --table 
aparcstatstable instead of --y. The output folder will have tables with 
lists of ROIs and p-values




On 7/30/16 5:33 PM, miracle ozzoude wrote:

Hey FreeSurfer experts,
Does anyone know the steps i have to perform if I want to conduct 
surface based thickness analysis using GLM but with ROI approach. 
Thank you very much.

Best,
Paul


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Re: [Freesurfer] Where are time series from adjusted (post selxavg3) ROIs

[Douglas Greve]

Run selxavg3-sess with -svres. This will create a new folder called 
"eres" in the output analysis directory where the residuals will be 
stored. Assuming that you have mapped your data to fsaverage space, you 
can then create a post cing label (mri_annotation2label) and  then use 
mri_segstats with --slabel fsaverage lh /path/to/postcing.label --id 1 
--avgwf avgwf.dat

The avgwf file will have the time course you want


On 7/30/16 2:40 AM, ERIK JAHNER wrote:
> Dear Freesurfer experts
>
>   I have been going through the documentation trying to figure out how to 
> extract the time series for an ROI (Posteriorcingulate) after removing the 
> regressors that I put in my mkanalysis-sess.  I have run the selxavg3.
> 1. Is this time course what is in the meanfunc.nii.gz?
> 2.  If it is, how do I pull this out in matrix format (.mat) out of the where 
> I basically get one mean adjusted value for the ROI at each timepoint? (e.g. 
> For the Posteriorcingulate, I want 210 values representing the mean 
> activation after removing the effect of my covariates wm and css for each of 
> the 210 timepoints).
> 3. Is this information in the X.mat file? If so, what is its location?
>
> Thanks
> Erik Jahner
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Re: [Freesurfer] Running Retinotopy in FSFAST, Design Matrix has Empty Regressors

[Douglas Greve]

Unfortunately, the way I have the retinotopy analysis set up, both polar 
and eccen must be there. However, you can just copy the polar into a new 
folder and call it eccen and it should complete. Then you can ignore the 
eccen part.



On 7/29/16 3:04 PM, Taylor, Johnmark wrote:

Hello,

I am trying to run a retinotopy analysis in fsfast, using only polar 
angle. However, when I try to run it, I am getting the error "Input to 
SVD must not contain NaN or Inf." I have traced this error and it 
looks like the design matrix X has 12 regressors (the first 12) that 
consist solely of zeros. I am using the following commands:


mkanalysis-sess -analysis retinotopy -fsd bold -runlistfile runlist.txt

-native -funcstem fmc -nuisreg mcextreg 3

-retinotopy 36.4 -per-session -paradigm retino.par -inorm

-spmhrf 0 -TR .650 -polyfit 2 -nskip 19


selxavg3-sess -analysis retinotopy -sf sublist.txt -df sessdir


Any idea what the first 12 regressors in the design matrix might 
correspond to in retinotopy analyses and why they'd be empty? I have 
looked at the documentation and there doesn't seem to be a clear 
labeling of the retinotopy design matrix anywhere, although perhaps 
I'm missing something.


Thank you very much,

JohnMark


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Re: [Freesurfer] Fwd: question about volume of mask

[Douglas Greve]

Hi Dorsa, please remember to include previous correspondence. I'm not 
sure what you are referring to, but when you reslice a volume, the size 
of the voxels usually changes so it is impossible to have exactly the 
same volume. Probably the original file is closest



On 7/29/16 12:08 PM, Dorsa Haji Ghaffari wrote:


Hi Bruce,

I was able to reslice the thalamus mask correctly, but when I measure 
the volume of the resliced thalamus, is not the same as the original 
thalamus. I was wondering why that is happening and which volume is 
more accurate. I appreciate any suggestions. I have attached both 
masks. Also can you tell me how to measure the volume of the resliced 
thalamus in Freesurfer?


Thank you

Dorsa



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Re: [Freesurfer] ALE map to surface

[Douglas Greve]

You need to run recon-all on the MNI152 T1 brain, then run mri_vol2surf 
passing your activation map to --mov  and with --regheader, then run 
freeview to visualize



On 8/1/16 6:38 PM, Carla Ammons wrote:

Hi!

I am new to freesurfer so this may be a basic question. I have an 
activation map (.nii) created via ALE meta-analysis in MNI space that 
I want to visualize on the surface. Do I use bbregister for this?


Thanks!
Carla


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Re: [Freesurfer] Creating contrast between two groups, controlling for 2 categorical(gender, scanner) and one continous variable(age)

[Douglas Greve]

The contrasts are correct. I think you have done the right thing (or as 
good as you can) in controlling for the scanners.


On 8/1/16 10:46 AM, Oana Georgiana Rus wrote:


Dear FreeSurfer Experts,

I want to compare structural measures(eg. thickness) between patients 
and controls controling for the effects of age, gender and scanner 
(parts of sample were scanned in scanner 1 parts in scanner 2).


I want to answer the question: *do patients and controls differ 
significantly in lGI when controlling for age (continous variable), 
gender(male/female), scanner(scanner1/scanner2)?*


*so i have to categorical (gender, scanner) and one continous variable 
to control for.*


*my FSGD file looks like:*

/GroupDescriptorFile 1 //
//Class PatientFemaleScanner1//
//Class PatientFemaleScanner2//
//Class PatientMaleScanner1//
//Class PatientMaleScanner2//
//Class ControlFemaleScanner1//
//Class ControlFemaleScanner2//
//Class ControlMaleScanner1//
//Class ControlMaleScanner2//
//Variables Age //
//Inputsubject1ControlMaleScanner123.6//
//Inputsubject2ControlFemaleScanner237.7//
//Inputsubject3   PatientFemaleScanner132.6/

...

*Total I would have 16 regressors with following contrasts:
*

*first conrast:* is there a difference in structural measure(eg. 
thickness) between *patients and controls* controlling for gender, 
scanner, age?


0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0

*second contrast:* is there a difference between the two scanners 
*scanner 1 and 2* controlling for effects of gender, age and group?


0.25 -0.25 0.25 -0.25 0.25 -0.25 0.25 -0.25 0 0 0 0 0 0 0 0

*Questions:*

  * Are the Contrasts created ok?
  * How could I control better for the effect of scanner, as part of
the sample was scanned with scanner 1 another part with scanner 2?

Thank you very much for your help!

Geo





--
Oana Georgiana Rus
PhD Student
Neuroimaging Center TUM-NIC
Klinikum rechts der Isar
Technische Universität München
Einsteinstr.1
81675 München
Raum 5.8

Tel. 089 4140 7971


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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Douglas Greve]

ps. you can always just load the xyz in the label into matlab and 
compute the centroid



On 8/1/16 10:23 AM, Sabin Khadka wrote:

Anyone?

Cheers,
Sabin Khadka

On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka 
mailto:mr.sabinkha...@gmail.com>> wrote:


Hi Doug, I tried to pick up from the thread below to get MNI
coordinates of each destrieux parcellation region.


https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html

I created label files from
mri_annotation2label --subject fsaverage --hemi lh(/rh)
--annotation aparc.a2009s --outdir label_destrieux   # which works
fine

And I tried to get the coordinates of each labels using

mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness
--clabel  --sum  --centroid --thmin 0
--hemi lh --subject fsaverage

But, all left labels would produce the same coordinates and so
does right labels. (I've attached few example files here with).
Also, it says TalX, TalY, TalZ are these coordinates in MNI or
Talairach?

Thanks for help.




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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Douglas Greve]

Try setting thmin to something small but non-zero (eg, 10e-6)


On 8/1/16 10:23 AM, Sabin Khadka wrote:

Anyone?

Cheers,
Sabin Khadka

On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka 
mailto:mr.sabinkha...@gmail.com>> wrote:


Hi Doug, I tried to pick up from the thread below to get MNI
coordinates of each destrieux parcellation region.


https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html

I created label files from
mri_annotation2label --subject fsaverage --hemi lh(/rh)
--annotation aparc.a2009s --outdir label_destrieux   # which works
fine

And I tried to get the coordinates of each labels using

mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness
--clabel  --sum  --centroid --thmin 0
--hemi lh --subject fsaverage

But, all left labels would produce the same coordinates and so
does right labels. (I've attached few example files here with).
Also, it says TalX, TalY, TalZ are these coordinates in MNI or
Talairach?

Thanks for help.




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Re: [Freesurfer] Long seg for hippo subfields

[Martin Reuter]

Hi Adam,
yes, a newer version is hiding.
Best, Martin

P.S. it is still unclear if this will make it into 6.0. But if we get 
lucky with a long delay of the release, the chances will significantly 
increase ;-)


On 08/01/2016 06:50 PM, Thomas, Adam (NIH/NIMH) [E] wrote:
> This look very cool:
> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields
>
>
> But the flag is not being recognized by recon-all using the most recent
> build:
>
> [adamt@felix scratch]$ cat $FREESURFER_HOME/build-stamp.txt
> freesurfer-Linux-centos6_x86_64-dev-20160730-bda65ec
> [adamt@felix scratch]$ recon-all -long-hippocampal-subfields-T1 md105Templ
> -hsfTP md105-1.long.md105Templ -hsfTP md105-2.long.md105Templ -hsfTP
> md105-3.long.md105Templ -hsfTP md105-4.long.md105Temp1 -hsfTP
> md105-5.long.md105Templ
>
> ERROR: Flag -long-hippocampal-subfields-T1 unrecognized.
> -long-hippocampal-subfields-T1 md105Templ -hsfTP md105-1.long.md105Templ
> -hsfTP md105-2.long.md105Templ -hsfTP md105-3.long.md105Templ -hsfTP
> md105-4.long.md105Temp1 -hsfTP md105-5.long.md105Templ
> Linux felix.nimh.nih.gov 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12
> 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s  exited with ERRORS at Mon Aug  1 18:42:51 EDT 2016
>
> For more details, see the log file
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> [adamt@felix scratch]$ uname -a
> Linux felix.nimh.nih.gov 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12
> 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
> [adamt@felix scratch]$ which recon-all
> /data/adamt/Apps/fs6-2016-07-31/bin/recon-all
> [adamt@felix scratch]$
>
> Is there a newer version of recon-all hiding somewhere?
>
>
> Thanks,
> -Adam
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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>
>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] Long seg for hippo subfields

[Thomas, Adam (NIH/NIMH) [E]]

This look very cool:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields


But the flag is not being recognized by recon-all using the most recent
build:

[adamt@felix scratch]$ cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos6_x86_64-dev-20160730-bda65ec
[adamt@felix scratch]$ recon-all -long-hippocampal-subfields-T1 md105Templ
-hsfTP md105-1.long.md105Templ -hsfTP md105-2.long.md105Templ -hsfTP
md105-3.long.md105Templ -hsfTP md105-4.long.md105Temp1 -hsfTP
md105-5.long.md105Templ

ERROR: Flag -long-hippocampal-subfields-T1 unrecognized.
-long-hippocampal-subfields-T1 md105Templ -hsfTP md105-1.long.md105Templ
-hsfTP md105-2.long.md105Templ -hsfTP md105-3.long.md105Templ -hsfTP
md105-4.long.md105Temp1 -hsfTP md105-5.long.md105Templ
Linux felix.nimh.nih.gov 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12
18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s  exited with ERRORS at Mon Aug  1 18:42:51 EDT 2016

For more details, see the log file
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

[adamt@felix scratch]$ uname -a
Linux felix.nimh.nih.gov 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12
18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
[adamt@felix scratch]$ which recon-all
/data/adamt/Apps/fs6-2016-07-31/bin/recon-all
[adamt@felix scratch]$

Is there a newer version of recon-all hiding somewhere?


Thanks,
-Adam



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[Freesurfer] ALE map to surface

[Carla Ammons]

Hi!

I am new to freesurfer so this may be a basic question. I have an
activation map (.nii) created via ALE meta-analysis in MNI space that I
want to visualize on the surface. Do I use bbregister for this?

Thanks!
Carla
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[Freesurfer] Poor automatic segmentation of the cerebellum

[Sam Mathias]

Dear list,

I'm interested in measuring cerebellar volumes using freesurfer. However,
the automatic segmentation (aseg) seems to be doing a poor job of capturing
the whole structure for many subjects. Specifically, it is chopping off the
bottom of the cerebellum. Here is an example:

https://drive.google.com/open?id=0B68CY3v4cg7tS0hSNkVVMWNiZV8xYWR2eTJQQlhFeVM0Q2Jn

The issue seems to be when the cerebellum is very close to the bottom of
the image, as is the case in many of our scans. Has anyone encountered
similar issues with cerebellum segmentation, and if so, have any advice
about how to improve it?

Many thanks,

--
Samuel R. Mathias, Ph.D.
Associate Research Scientist (ARS)
Neurocognition, Neurocomputation and Neurogenetics (n3) Division
Yale University School of Medicine
40 Temple Street, Room 694
New Haven CT 06511
http://www.srmathias.com
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Re: [Freesurfer] mris_label2annot

[Bruce Fischl]

Hi Caroline

the colortables are in $FREESURFER_HOME. Usually we use

$FREESURFER_HOME/FreeSurferColorLUT.txt

cheers
Bruce


On Mon, 1 Aug 2016, Caroline Beelen wrote:



Dear FS,

 

Sorry to bother again, but I’m currently in need for some quick help.

Today, I also ran into another problem. I tried to display only few ROI’s in
Freeview instead of the whole brain. Therefore, I tried to create a new
annotation file consisting of only few labels (from regions of DK-atlas) and
I used the mri_annotation2label on my own created fsaverage to get these
labels. This worked fine.

Then I used the command of mris_label2annot to create the annotation file,
but part of the command, --ctab aparc.annotation.ctab, is not recognized.
Replacing it by –ctab  fsaverage/label/lh.aparc.annot (file exists in the
label folder of fsaverage) gives me the following error: CTABreadASCII:
badly formed file. ERROR: reading fsaverage/label/lh.aparc.annot. I couldn’t
find, or create, any other aparc.annot file.

 

What would be the right command (for the part of ctab) to get
mris_label2annot working? Or is there perhaps a better way to only display
certain ROI’s in Freeview? (the latter I could still explore but assistance
is certainly appreciated)

 

Thanks a lot!

Caroline

 

 


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Re: [Freesurfer] freesurfer 6.0 release date

[Bruce Fischl]

Hi Fengji

we have frozen the code and are going through various tests now so are 
hoping sometime in the next few weeks, but of course it's impossible to say 
as it depends on how well the tests turn out.


cheers
Bruce


On Mon, 1 
Aug 2016, Fengji Geng wrote:



Hi fs developers, 
I am wondering if you have any estimation when fs 6.0 will come out.  The
reason that I ask this is because we are running some analysis using fs 5.1
and planning to switch to a more recent version of fs. If fs 6.0 will come
out soon, we will probably hold and wait for it. If not, we will just switch
to fs 5.3. 

Thanks!

--
Fengji Geng

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Re: [Freesurfer] Freesurfer dev version

[Iglesias, Eugenio]

Hi Daniel,
The issue is fixed, but I don’t know if the updated version is already in dev.
Zeke, can you shed some light on this?
Cheers,
/Eugenio

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


On 1 Aug 2016, at 19:49, Liu, Daniel mailto:d...@mcw.edu>> wrote:

It was the invalid MEX file problem mentioned in this exchange 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48412.html

I was told it would be fixed sometime this week in the dev version (and in 2 
weeks when the next beta version was released).

Thanks,

Daniel

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>>
Sent: Monday, August 1, 2016 11:04 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer dev version

which error? The mri_normalize problem? If so, then yes I believe that is
now fixed
On Mon, 1 Aug 2016, Liu, Daniel wrote:

Hi,


I wanted to follow up on the error that came up in the freesurfer dev version 
this past week.  Has it been fixed yet?  If so, has the link to the download 
page been changed?  The one I booked marked does not lead me to the page 
anymore and I would appreciate it if you could direct me to the correct 
location.


Thanks,


Daniel

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Re: [Freesurfer] Freesurfer dev version

[Liu, Daniel]

It was the invalid MEX file problem mentioned in this exchange 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48412.html

I was told it would be fixed sometime this week in the dev version (and in 2 
weeks when the next beta version was released).

Thanks,

Daniel

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Monday, August 1, 2016 11:04 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer dev version

which error? The mri_normalize problem? If so, then yes I believe that is
now fixed
On Mon, 1 Aug 2016, Liu, Daniel wrote:

> Hi,
>
>
> I wanted to follow up on the error that came up in the freesurfer dev version 
> this past week.  Has it been fixed yet?  If so, has the link to the download 
> page been changed?  The one I booked marked does not lead me to the page 
> anymore and I would appreciate it if you could direct me to the correct 
> location.
>
>
> Thanks,
>
>
> Daniel
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] freesurfer 6.0 release date

[Fengji Geng]

Hi fs developers,

I am wondering if you have any estimation when fs 6.0 will come out.  The
reason that I ask this is because we are running some analysis using fs 5.1
and planning to switch to a more recent version of fs. If fs 6.0 will come
out soon, we will probably hold and wait for it. If not, we will just
switch to fs 5.3.

Thanks!

-- 
Fengji Geng
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[Freesurfer] Cannot launch freeview

[Da, Xiao]

Hi Freesurfer Developers,

I tried to run freeview but got this following error message.
freeview.bin: error while loading shared libraries: libXss.so.1: cannot open 
shared object file: No such file or directory

Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Linux version:
NAME="Red Hat Enterprise Linux Workstation"
VERSION="7.2 (Maipo)"
ID="rhel"
ID_LIKE="fedora"
VERSION_ID="7.2"
PRETTY_NAME="Red Hat Enterprise Linux"

I tried "locate libXss.so.1", but returned nothing.

Please let me know if you have the solution to fix this error.

Thanks and best regards,

Xiao Da
Biomedical Engineer - Programmer Analyst II
Functional Neuroimaging Laboratory
Brigham and Women's Hospital
221 Longwood Avenue, Braunwald Building, Room LM116
Boston, MA 02115
x...@bwh.harvard.edu






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Re: [Freesurfer] Freesurfer dev version

[Bruce Fischl]

which error? The mri_normalize problem? If so, then yes I believe that is 
now fixed
On Mon, 1 Aug 2016, Liu, Daniel wrote:

> Hi,
>
>
> I wanted to follow up on the error that came up in the freesurfer dev version 
> this past week.  Has it been fixed yet?  If so, has the link to the download 
> page been changed?  The one I booked marked does not lead me to the page 
> anymore and I would appreciate it if you could direct me to the correct 
> location.
>
>
> Thanks,
>
>
> Daniel
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] Freesurfer dev version

[Liu, Daniel]

Hi,


I wanted to follow up on the error that came up in the freesurfer dev version 
this past week.  Has it been fixed yet?  If so, has the link to the download 
page been changed?  The one I booked marked does not lead me to the page 
anymore and I would appreciate it if you could direct me to the correct 
location.


Thanks,


Daniel

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[Freesurfer] mris_label2annot

[Caroline Beelen]

Dear FS,

Sorry to bother again, but I'm currently in need for some quick help.
Today, I also ran into another problem. I tried to display only few ROI's in 
Freeview instead of the whole brain. Therefore, I tried to create a new 
annotation file consisting of only few labels (from regions of DK-atlas) and I 
used the mri_annotation2label on my own created fsaverage to get these labels. 
This worked fine.
Then I used the command of mris_label2annot to create the annotation file, but 
part of the command, --ctab aparc.annotation.ctab, is not recognized. Replacing 
it by -ctab  fsaverage/label/lh.aparc.annot (file exists in the label folder of 
fsaverage) gives me the following error: CTABreadASCII: badly formed file. 
ERROR: reading fsaverage/label/lh.aparc.annot. I couldn't find, or create, any 
other aparc.annot file.

What would be the right command (for the part of ctab) to get mris_label2annot 
working? Or is there perhaps a better way to only display certain ROI's in 
Freeview? (the latter I could still explore but assistance is certainly 
appreciated)

Thanks a lot!
Caroline


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[Freesurfer] Creating contrast between two groups, controlling for 2 categorical(gender, scanner) and one continous variable(age)

[Oana Georgiana Rus]

Dear FreeSurfer Experts,

I want to compare structural measures(eg. thickness) between patients 
and controls controling for the effects of age, gender and scanner 
(parts of sample were scanned in scanner 1 parts in scanner 2).


I want to answer the question: *do patients and controls differ 
significantly in lGI when controlling for age (continous variable), 
gender(male/female), scanner(scanner1/scanner2)?*


*so i have to categorical (gender, scanner) and one continous variable 
to control for.*


*my FSGD file looks like:*

/GroupDescriptorFile 1 //
//Class PatientFemaleScanner1//
//Class PatientFemaleScanner2//
//Class PatientMaleScanner1//
//Class PatientMaleScanner2//
//Class ControlFemaleScanner1//
//Class ControlFemaleScanner2//
//Class ControlMaleScanner1//
//Class ControlMaleScanner2//
//Variables Age //
//Inputsubject1ControlMaleScanner123.6//
//Inputsubject2ControlFemaleScanner237.7//
//Inputsubject3   PatientFemaleScanner132.6/

...

*Total I would have 16 regressors with following contrasts:
*

*first conrast:* is there a difference in structural measure(eg. 
thickness) between *patients and controls* controlling for gender, 
scanner, age?


0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0

*second contrast:* is there a difference between the two scanners 
*scanner 1 and 2* controlling for effects of gender, age and group?


0.25 -0.25 0.25 -0.25 0.25 -0.25 0.25 -0.25 0 0 0 0 0 0 0 0

*Questions:*

 * Are the Contrasts created ok?
 * How could I control better for the effect of scanner, as part of the
   sample was scanned with scanner 1 another part with scanner 2?

Thank you very much for your help!

Geo





--
Oana Georgiana Rus
PhD Student
Neuroimaging Center TUM-NIC
Klinikum rechts der Isar
Technische Universität München
Einsteinstr.1
81675 München
Raum 5.8

Tel. 089 4140 7971

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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Sabin Khadka]

Anyone?

Cheers,
Sabin Khadka

On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka 
wrote:

> Hi Doug, I tried to pick up from the thread below to get MNI coordinates
> of each destrieux parcellation region.
>
>
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html
>
> I created label files from
> mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation
> aparc.a2009s --outdir label_destrieux   # which works fine
>
> And I tried to get the coordinates of each labels using
>
> mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel
>  --sum  --centroid --thmin 0
> --hemi lh --subject fsaverage
>
> But, all left labels would produce the same coordinates and so does right
> labels. (I've attached few example files here with). Also, it says TalX,
> TalY, TalZ are these coordinates in MNI or Talairach?
>
> Thanks for help.
>
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Re: [Freesurfer] mri_label2label error

[Bruce Fischl]

Hi > Domenico

I think the problem is that you have a forward slash in your subject 
name, as well as your SUBJECTS_DIR and FREESURFER_HOME. Did you perhaps but 
them inside double quotes or something? Usually the forward slash \ let's 
you extend command over multiple lines, but in this case it appears to have 
been included as part of the names themsevles. Or maybe you included two of 
them in a row (\\)?


cheers
Bruce


On Mon, 1 Aug 2016, Aquino Domenico wrote:



Dear Freesurfer team,


I'm trying to segment a pre-processed 3D PSIR volume.

Everything seems to work correctly, however at the end of recon-all something 
goes wrong.

The command "mri_label2label" returns the ERROR "No such file or directory\ 
mri_label2label: could not open label file...". Actually the file has not been
created but I don't understand why. I checked the path for special characters, 
I checked the permissions and so on and it seems all ok.

Which could be the issue?


In attachment you'll find the recon-all.log file.


Thanks a lot,


Domenico


___
Eng. Domenico Aquino
Department of Neuroradiology
IRCCS Foundation Neurological Institute "Carlo Besta"
Via Celoria,11-20133 Milano
Phone: +39 02 23942472
Fax +39 02 23942543

1463859753944_LogoWhite.jpg

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[Freesurfer] Fw: Running recon-all with T1 and FLAIR

[Silas]

Dear FreeSurfer team,


I'm doing a structural analysis with 50 MS patients and 50 healthy controls 
(T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white 
matter. My co-worker did manual editing (bullet points) in the FLAIR images, 
and i would like to use these edits when running recon-all in order to avoid 
further manual editing.


The data i'm working with is already resliced to 1 mm and co-registered in 
MNI-space.

1) Can i use this data or would it be preferable to use the original T1's?


My thought was to run the following command:

recon-all -subject subjectname -i /path/to/input_volume -FLAIR 
/path/to/FLAIR_volume_with_edits -FLAIRpial -all

2) Does this look correct? Is there anything i should be aware of? -> update: 
Does this command only improve the pial surface? How can i also improve the 
white mater segmentation (white) using FLAIR corrections?

3) Does it make a difference running recon-all -all with the FLAIR image - 
compared to running recon-all -autorecon3 with the FLAIR after running 
recon-all -all with only the T1?

4) I've also thought about using the lesion segmentation toolbox for SPM and 
completely avoid manual editing - is this preferable to using the FLAIR with 
manual editing?

5) How is the general strength of analysing corpus callosum structurally in MS 
patients using FreeSurfer?


Best, Silas
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Re: [Freesurfer] How does Optseq2 arrange order of conditions?

[連 志浩]

Dear Douglas,

Thanks for your explanation. These information are helpful to me.



>I'm not sure what you mean. How can it be a delay if it is after the trial is 
>over?

I’m sorry for I didn’t describe my second question well. I think I can take 
another situation to describe my question.

If I have a experiment that present stimulus until participants response, and I 
know the average RT of this experiment is 1500 ms after pilot test.

In this situation, should I +/- the duration of jitter/null condition in terms 
of the duration of each stimulus?

For example, if a part of sequence Optseq2 output is “ Con1 Null(500 ms) Con2 
Null(1500 ms)”, and one of participants takes 1000 ms to response for Con1.

Should I add 500 ms to the first Null? or I don’t need to anything?

Thanks for your reading.

Best Regards,
Chih-Hao

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[Freesurfer] significance overlay Freeview

[Caroline Beelen]

Dear FS,

Yes, I'm running FS 5.3. :)
How can I visualize the significance overlay (correctly)?  Which command should 
I use to view a significance overlay in freeview in FS 5.3? See also my email 
below.

Thank you very much in advance!
Best, Caroline

Hi Caroline,

Are you running FS 5.3? The command on the webpage is based on the upcoming 
6.0, I believe. So some of the command line options are not available in 5.3.

Best,
Ruopeng

> On Jul 29, 2016, at 9:11 AM, Caroline Beelen 
> mailto:caroline.bee...@kuleuven.be>> wrote:
>
> Dear FS team,
>
> Apologies in advance for perhaps again a rather basic question. I attempted 
> to load the aparc overlay in freeview by using the written command from the 
> group analysis page, however it failed to load correctly.
>
> I used the following command:
> freeview -f 
> fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5
>  -viewport 3d
> ? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis 
> and dyslect is the contrast folder within this file (main effect of 
> dyslexia), containing a sig.mgh file (all seems fine)
>
> Unfortunately, I got an error that it does not recognize 
> overlay_treshold=4,5. I used freeview ?h and tried certain commands alike, 
> but they didnt work. When leaving out this part, I got another error that it 
> failed to recognize annot_outline=1. Again, leaving this out too, freeview 
> loads itself and the DK-regions become visible. However, nothing else seems 
> to get activated, and even not when putting configure overlay (which is set 
> to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens.
> When looking at the command line it says that it implemented the colortable 
> of DK-atlas (even twice), but it tells me nothing else. Also, after closing 
> and reloading Freeview by using the similar command and then clicking on 
> configure overlay the screen sometimes gets stuck, giving me the impression 
> that something must be wrong with the command.
>
> Could you please help me out and provide me the right command-line for 
> loading the overlay of the significance map of 
> roi.lh.area.dyslect_basic.glmdir/dyslect?
>
> Thanks in advance!
>
> Kind regards, Caroline
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Phd-candidate KU Leuven
Gezins-en Orthopedagogiek
Vanderkelenstraat 32, 3000 Leuven
Belgium

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