Re: [Freesurfer] slice timing correction fmcstc files are lacking

[stdp82]

Hi using Philips scanner (interleaved)Therefore, I'm running
preproc-sess -sf sessid -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest 
-per-run -sliceorder odd
However, as you can see below stc has been not produced.

file:///Applications/freesurfer/subjects/Sess101/rest/001/f.niifile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.mat.aff12.1Dfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.mcdatfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.nii.gz.mclogfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.nii.gz.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.sm5.fsaverage.lh.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.sm5.fsaverage.rh.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.odd.sm5.mni305.1mm.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.sm5.fsaverage.lh.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.sm5.fsaverage.rh.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/fmcpr.sm5.mni305.2mm.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/global.meanval.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/global.waveform.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/init.register.dof6.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_Amygdala.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_Amygdala.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_orbitofrontal.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_orbitofrontal.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_Thalamus.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/L_Thalamus.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/masks/file:///Applications/freesurfer/subjects/Sess101/rest/001/mcdat2extreg.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/mcprextregfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_Amygdala.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_Amygdala.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_orbitofrontal.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_orbitofrontal.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_Thalamus.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/R_Thalamus.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.mincostfile:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.paramfile:///Applications/freesurfer/subjects/Sess101/rest/001/register.dof6.dat.sumfile:///Applications/freesurfer/subjects/Sess101/rest/001/template.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/template.nii.gzfile:///Applications/freesurfer/subjects/Sess101/rest/001/vcsf.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/vcsf.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/vcsf.dat.pca-stats.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/wm.datfile:///Applications/freesurfer/subjects/Sess101/rest/001/wm.dat.logfile:///Applications/freesurfer/subjects/Sess101/rest/001/wm.dat.pca-stats.dat
Thanks,

Stefano
what slice order was the data created with? Find out and then use that slice 
order in the commandOn 8/26/15 4:14 AM, std...@virgilio.it wrote:
Hi list,I'm performing slice time correction on preproc-sess -s Sess201 -fwhm 5 
-surface fsaverage lhrh -mni305-1mm -fsd rest -per-run. I have acquired data 
using a Philipps scanner (interleaved). Thefore, shuold I use "-sliceorder 
siemens"?The command line:
preproc-sess -s Sess201 -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest 
-per-run -sliceorder siemensproduces the files reported below.

fmcstc files are lacking. Please, give me an help.

Thanks,

Stefano


file:///Applications/freesurfer/subjects/Sess201/rest/001/f.nii
file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.mat.aff12.1D
file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.mcdat
file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.nii.gz
file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.nii.gz.mclog
file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.siemens.nii.gz
file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.siemens.nii.gz.log
file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.siemens.sm5.fsaverage.lh.nii.gz
file:///Applications/freesurfer/subjects/Sess201/rest/001/fmcpr.siemens.sm5.fsaverage.rh.nii.gz

Re: [Freesurfer] two functions' purpose and usage

[Yun Wang]

Anyone knows this? 


> On Sep 2, 2015, at 11:12, Yun Wang  wrote:
> 
> Hi all experts,
> 
> 
> I have questions about two functions purposes and usages. 
> 
> 
> mri_compute_layer_fractions and mris_compute_layer_intensities. 
> 
> 
> mri_compute_layer_fractions [options]   
> 
> 1   Which registration file ?
> 2  which input volume?
> 3 options?
> mris_compute_layer_intensities [options]   volume fractions file>  
> 
> 1 input intensity volume means fMRI ?
> 
> 
> Appreciate your idea! 
> 
> 
> Yun Wang
> 
> 

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Re: [Freesurfer] Freesurfer ROI

[Lim, Lena]

Sorry, I haven't heard any replies so am re-posting this again for help please:


Dear Experts,

I have 3 groups: A, PC, HC

I did a VBM analysis in SPM and found group differences in grey matter volume 
in 2 clusters:
1) Bilateral pre-/SMA, left middle/superior frontal gryi
2) left inferior/middle temporal/fusiform/inferior/middle occipital 
gyri/superior/inferior posterior cerebellar lobe

Is there any way I can use the SPM images to extract these ROI regions to see 
if they differ in cortical thickness and surface area please?

Many thanks,

Lena


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[Freesurfer] recon-all

[John Anderson]

Hi freesurfers,

I am interested in studying the difference between the outer and deep white matter volume in my study groups.

I am thinking in the following procedures:

1. If there is any way in Freesurfer to do segmentation for the white matter (only in the depth of 3 cm) starting from the cortex. Then  second segmentation for the deep white matter.

2. Creating a mask ( using mri_binarize) for all the superficial white matter Freesurfer's labels and another mask for the deep white matter  ( how can I find the Freesurfer  deep white matter labels and the outer white matter labels ?)

3. If there is any atlas that can separate the outer and deep white matter then do the segmentation depending on this new atlas.

 

 

Thanks in advance for any suggestion,

John 


 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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Re: [Freesurfer] Freesurfer ROI

[Bruce Fischl]

Hi Lena
Sure, but you will need to run all your subjects through recon-all first. The 
if the ROI is in MNI space you can use mri_label2label to map it to our group 
space fsaverage.
Cheers
Bruce


> On Sep 4, 2015, at 9:27 AM, Lim, Lena  wrote:
> 
> Sorry, I haven’t heard any replies so am re-posting this again for help 
> please:
>  
>  
> Dear Experts,
>  
> I have 3 groups: A, PC, HC
>  
> I did a VBM analysis in SPM and found group differences in grey matter volume 
> in 2 clusters:
> 1) Bilateral pre-/SMA, left middle/superior frontal gryi
> 2) left inferior/middle temporal/fusiform/inferior/middle occipital 
> gyri/superior/inferior posterior cerebellar lobe
>  
> Is there any way I can use the SPM images to extract these ROI regions to see 
> if they differ in cortical thickness and surface area please?  
>  
> Many thanks,
>  
> Lena
>  
>  
> ___
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[Freesurfer] conjunction map

[stdp82]

Hi list,
is possible to obtained a conjunction map from vlrmerge command on FS-FAST 
(resting state) results?

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Re: [Freesurfer] Freesurfer ROI

[Lim, Lena]

Thanks, Bruce. I ran the recon-all for all subjects before and then did the 
group analysis using the mri-glmfit command and qdec. Sorry, I don’t quite 
understand. What exact command do I use?

Mri_label2label  --srcsubject fsaverage --srclabel fsaverage/label/(spm roi 
image file names?)  --trgsubject PAC01 PAC02 PAC03…PAC70 –trglabel PAC01 
PAC02.. PAC70/label/(spm roi image file names?)  --hemi lh –regmethod surface

How do I next do the group comparison on the ROI?

Many thanks again,

Lena


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 04 September 2015 15:25
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer ROI

Hi Lena
Sure, but you will need to run all your subjects through recon-all first. The 
if the ROI is in MNI space you can use mri_label2label to map it to our group 
space fsaverage.
Cheers
Bruce

On Sep 4, 2015, at 9:27 AM, Lim, Lena 
> wrote:
Sorry, I haven’t heard any replies so am re-posting this again for help please:


Dear Experts,

I have 3 groups: A, PC, HC

I did a VBM analysis in SPM and found group differences in grey matter volume 
in 2 clusters:
1) Bilateral pre-/SMA, left middle/superior frontal gryi
2) left inferior/middle temporal/fusiform/inferior/middle occipital 
gyri/superior/inferior posterior cerebellar lobe

Is there any way I can use the SPM images to extract these ROI regions to see 
if they differ in cortical thickness and surface area please?

Many thanks,

Lena


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[Freesurfer] Elusive skull strip

[CHESTER DOLPH]

Hello,

I have one brain in a large dataset that is not skull stripping properly.
I have tried the changing watershed parameters using the freesurfer
tutorial, but brainmask.mgz does not seem to change and I am receiving this
error:

"  The surface validation has detected a possible Error
  If the final segmentation is not valid,
  try using the option '-atlas'"

I tried gcut but it removed too much brain.  I am aware that tkmedit
enables manual editing but prefer to use the Brainsuite GUI.

If I want to use primarily  Freesurfer , may I augment  brainmask.mgz using
Brainsuite and then resume the recon pipeline?  I am concerned that this
would disrupt other files (e.g. brainmask.auto.mgz).

Thanks,
Chester

the skull strip command that I explored (tried various wsthresh values):

$ recon-all -subjid [removed] -skullstrip -wsthresh -20 -clean-bm
-no-wsgcaatlas
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[Freesurfer] ERROR: loading aseg $SUBJ/mri/MRS_MASK.nii.gz.mgz

[stdp82]

Hi list,I'm performing FS-FAST using as seed MRS voxel (MRS_MASK). MRS_MASK 
shows a god overlap with orig and both of these are located in 
$SUBJ/mri.Firstly, I have performed:fcseed-config -segid 1 -seg MRS_MASK.nii.gz 
-fsd rest -mean -cfg mean.MRS_MASK.configNext,fcseed-sess -s Sess101 -cfg 
mean.MRS_MASK.configproducing this error:mghRead( 
$SUBJ/mri/MRS_MASK.nii.gz.mgz, -1): could not open file
ERROR: loading aseg $SUBJ/mri/MRS_MASK.nii.gz.mgzWhich is the 
error?ThanksStefano
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[Freesurfer] mri_glmfit-sim error

[Xiaomin Yue]

Hi,
I got this error when run mri_glmfit-sim: missing name for redirect.  I am 
running freesurfer 5.3.  the command is: mri_glmfit --glmdir ces.nii --cache 2 
--sim-sign .  The ces.nii was generated from group level analysis 
(isxconcat-sess).  
Thanks for your help.
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Re: [Freesurfer] Problem running Tracula

[Anastasia Yendiki]

Hi Andrea - Make sure that the b-value table and gradient table are saved 
as plain text files. When you run the "more" command on them, you should 
see all the numbers and only numbers.


This is what I get when I run more on your files (this may vary depending 
on the flavor of unix you have on your computer):


% more bvals.txt
0^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000
^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M1000^M^M1000^M1000^M1000^M1000^M1000^M1000
% more bvecs.txt
"bvecs.txt" may be a binary file.  See it anyway?
??0^@ ^@0^@ ^@0^@^M^@
^@-^@1^@ ^@0^@ ^@0^@^M^@
^@0^@ ^@-^@1^@ ^@0^@^M^@
^@0^@ ^@0^@ ^@1^@^M^@
^@0^@.^@0^@4^@2^@ ^@0^@.^@1^@1^@5^@ ^@-^@0^@.^@9^@9^@3^@^M^@
^@-^@0^@.^@1^@7^@5^@ ^@0^@.^@2^@ ^@-^@0^@.^@9^@6^@4^@^M^@
^@-^@0^@.^@2^@3^@2^@ ^@0^@.^@1^@6^@3^@ ^@-^@0^@.^@9^@5^@9^@^M^@
^@-^@0^@.^@3^@6^@8^@ ^@-^@0^@.^@0^@2^@6^@ ^@-^@0^@.^@9^@3^@^M^@
^@-^@0^@.^@1^@9^@ ^@-^@0^@.^@3^@7^@4^@ ^@-^@0^@.^@9^@0^@8^@^M^@
^@0^@.^@1^@1^@7^@ ^@-^@0^@.^@8^@3^@3^@ ^@-^@0^@.^@5^@4^@^M^@
^@0^@.^@2^@ ^@-^@0^@.^@2^@5^@3^@ ^@-^@0^@.^@9^@4^@7^@^M^@
^@0^@.^@4^@9^@6^@ ^@-^@0^@.^@1^@3^@4^@ ^@-^@0^@.^@8^@5^@8^@^M^@
^@0^@.^@0^@1^@4^@ ^@0^@.^@6^@2^@8^@ ^@-^@0^@.^@7^@7^@8^@^M^@
^@0^@.^@7^@4^@4^@ ^@0^@.^@1^@4^@8^@ ^@-^@0^@.^@6^@5^@1^@^M^@
^@0^@.^@7^@6^@1^@ ^@-^@0^@.^@3^@2^@ ^@-^@0^@.^@5^@6^@4^@^M^@
^@0^@.^@1^@8^@1^@ ^@-^@0^@.^@9^@2^@5^@ ^@-^@0^@.^@3^@3^@5^@^M^@
^@0^@.^@6^@8^@ ^@0^@.^@4^@2^@2^@ ^@-^@0^@.^@6^@^M^@
^@-^@0^@.^@7^@7^@7^@ ^@-^@0^@.^@4^@7^@1^@ ^@-^@0^@.^@4^@1^@8^@^M^@
^@-^@0^@.^@9^@2^@4^@ ^@0^@.^@1^@0^@4^@ ^@-^@0^@.^@3^@6^@8^@^M^@
^@-^@0^@.^@4^@6^@8^@ ^@0^@.^@7^@6^@7^@ ^@-^@0^@.^@4^@3^@8^@^M^@
^@-^@0^@.^@8^@8^@2^@ ^@0^@.^@1^@8^@9^@ ^@-^@0^@.^@4^@3^@2^@^M^@
^@-^@0^@.^@6^@9^@ ^@-^@0^@.^@7^@0^@6^@ ^@-^@0^@.^@1^@5^@7^@^M^@
^@-^@0^@.^@2^@3^@9^@ ^@-^@0^@.^@7^@5^@7^@ ^@-^@0^@.^@6^@0^@8^@^M^@
^@0^@.^@0^@5^@8^@ ^@-^@0^@.^@9^@8^@4^@ ^@0^@.^@1^@7^@^M^@
^@0^@.^@5^@3^@7^@ ^@-^@0^@.^@8^@3^@6^@ ^@-^@0^@.^@1^@1^@3^@^M^@
^@0^@.^@9^@9^@2^@ ^@0^@.^@1^@2^@1^@ ^@-^@0^@.^@0^@4^@2^@^M^@
^@0^@.^@9^@9^@7^@ ^@-^@0^@.^@0^@7^@1^@ ^@-^@0^@.^@0^@3^@8^@^M^@
^@0^@.^@8^@7^@2^@ ^@-^@0^@.^@4^@7^@8^@ ^@-^@0^@.^@1^@0^@1^@^M^@
^@0^@.^@2^@4^@9^@ ^@-^@0^@.^@9^@3^@3^@ ^@0^@.^@2^@5^@8^@^M^@
^@-^@0^@.^@1^@1^@8^@ ^@-^@0^@.^@9^@9^@2^@ ^@-^@0^@.^@0^@4^@7^@^M^@
^@-^@0^@.^@3^@3^@8^@ ^@-^@0^@.^@8^@4^@1^@ ^@0^@.^@4^@2^@2^@^M^@
^@-^@0^@.^@5^@2^@9^@ ^@-^@0^@.^@8^@4^@1^@ ^@0^@.^@1^@1^@6^@^M^@
^@-^@0^@.^@9^@9^@7^@ ^@-^@0^@.^@0^@5^@5^@ ^@-^@0^@.^@0^@5^@7^@


On Fri, 4 Sep 2015, andrea cristina Lima wrote:


Please I am having the problem:

bvecs and bvals don't have the same number of entries


I tried to use the bvecs and bvals files as suggested in the Tutorial, but 
doesn't
work. Please see the files attached (log, files and script). Thank you very much




--
Andrea Cristina de Lima PardiniCV: http://lattes.cnpq.br/0921194840474573

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[Freesurfer] Cortical editing issues

[Deborrah Castillo]

Hi,

After doing cortical edits (removing part of the dura) and running RECON23,
the *pial (red line) and white surface (yellow line) are crossing each
other* (please see attached images) which are not present before the edits.
We know that this is not correct and we wanted to ask your inputs or
suggestions on what we could do to correct it.

*General Info:*
linux distribution = CentOS 4.6
-environment/version = freesurfer 5.3
-SUBJETCS_DIR = /apps/fs530/subjects
   **or**
/mnt/fs5/fs530/
-output of "which" = GNU v2.16
-current working directory = /mnt/home/username/scripts


Thank you.

Aloha,
Deborrah

-- 
-- 
University of Hawaii
John A. Burns School of Medicine
Department of Medicine
Neuroscience and Magnetic Resonance Research Program
Queens Medical Center, 7th Floor UH Tower
1356 Lusitana Street
Honolulu, HI 96813
Tel:+1-808-586-7488
Tel: +1808-586-7459

Fax:+1808-586-7465
Web: http://hawaii.edu/mri/home_v6.htm
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[Freesurfer] generating new FREESURFER directory from linear transform

[David Grayson]

Hi all,

I would like to take a single subject's freesurfer directory and apply a single 
linear transform (I already have the .dat file I would like to use) to all of 
the recon-all output (volumes, surfaces, label files, etc). Essentially I would 
like to apply the transform and make a new freesurfer directory that keeps as 
much of the same contents as possible. The transform is not just rigid-body, it 
includes scaling and skewing.

Is there a suggested way to do this, either all-at-once or piece-by-piece?

Thank you very much,

David

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Re: [Freesurfer] generating new FREESURFER directory from linear transform

[Bruce Fischl]

Hi David

I don't think there's an easy way to do it all at once unless you apply 
the transform to the orig.mgz then rerun recon-all (which will not be the 
same as applying it to the outputs)


sorry
Bruce
On Fri, 4 Sep 2015, David Grayson wrote:



Hi all,

 

I would like to take a single subject’s freesurfer directory and apply a
single linear transform (I already have the .dat file I would like to use)
to all of the recon-all output (volumes, surfaces, label files, etc).
Essentially I would like to apply the transform and make a new freesurfer
directory that keeps as much of the same contents as possible. The transform
is not just rigid-body, it includes scaling and skewing.

 

Is there a suggested way to do this, either all-at-once or piece-by-piece?

 

Thank you very much,

 

David

 


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