[Freesurfer] Mri_mask producing only zeros

[Sims, Sara A (Campus)]

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Freesurfers,
I am trying to use mri_mask using surface overlays. I made a label into a 
volume and then into a surface with 1s inside the label and 0s outside the 
label. I want to make a connectivity map surface overlay with values only 
within my label overlay. However when I run it, it creates a surface overlay 
with only zeros. There is definitely values within the label surface overlay (I 
triple checked).
Code I used:
Mri_mask original_surface_overlay label_mask new_masked_output

It doesn’t output any errors.
Sara A. Sims

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[Freesurfer] BIDS Governance and Steering Group election closing tomorrow!

[Franklin Feingold]

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Time is running out to vote on our BIDS Governance document 
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 Voting closes tomorrow October 15, 2019, at 11:59pm Pacific Daylight Time (UTC 
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Re: [Freesurfer] Mri_mask producing only zeros

[Bruce Fischl]

Hi Sara

we will need to know the actual commands and the screen output from them 
that you ran


cheers
Bruce

On Mon, 14 Oct 2019, Sims, Sara A (Campus) wrote:



External Email - Use Caution

Freesurfers,

I am trying to use mri_mask using surface overlays. I made a label into a
volume and then into a surface with 1s inside the label and 0s outside the
label. I want to make a connectivity map surface overlay with values only
within my label overlay. However when I run it, it creates a surface overlay
with only zeros. There is definitely values within the label surface overlay
(I triple checked).

Code I used:

Mri_mask original_surface_overlay label_mask new_masked_output

 

It doesn’t output any errors.

Here is what it looks like in freeview:

Original surface overlay (label is outlined in green)

[IMAGE]

The label made into a surface overlay (same  as the one shown in green
above):

[IMAGE]

But this is the output: all zeros even though there was data within the
mask.

[IMAGE]

 

Help!

Sara A. Sims

 


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Re: [Freesurfer] Mri_mask producing only zeros

[Sims, Sara A (Campus)]

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Here is how I made the label into a surface overlay:
mri_label2vol --label $label/lh.7Networks_6.label --temp 
/data/project/vislab/a/HCP_diff_Sara/fsaverage/mri/orig.mgz --identity --o 
$vols/lh.7Networks_6.nii 
mri_vol2surf --src $vols/lh.7Networks_6.nii --out $surfs/lh.7Networks_6.mgh 
--regheader fsaverage --hemi lh

Here is the mri_mask command:
mri_mask betamaskedFPcflh.mgh $surfs/lh.7Networks_6.mgh 
betasigandlabelmaskedFPcflh.mgh

Output from mri_mask:
DoAbs = 0
INFO: MRImask() using MRImaskDifferentGeometry()
Writing masked volume to betasigandlabelmaskedFPcflh.mgh...done.

Sara A. Sims, MA
Medical/Clinical Psychology Program
UAB | The University of Alabama at Birmingham
CIRC Suite 252A | 1719 6th Avenue South | Birmingham, AL 35294
P: 205.975.4060 | sno...@uab.edu 
 

On 10/14/19, 2:35 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

Hi Sara

we will need to know the actual commands and the screen output from them 
that you ran

cheers
Bruce

On Mon, 14 Oct 2019, Sims, Sara A (Campus) wrote:

> 
> External Email - Use Caution
> 
> Freesurfers,
> 
> I am trying to use mri_mask using surface overlays. I made a label into a
> volume and then into a surface with 1s inside the label and 0s outside the
> label. I want to make a connectivity map surface overlay with values only
> within my label overlay. However when I run it, it creates a surface 
overlay
> with only zeros. There is definitely values within the label surface 
overlay
> (I triple checked).
> 
> Code I used:
> 
> Mri_mask original_surface_overlay label_mask new_masked_output
> 
>  
> 
> It doesn’t output any errors.
> 
> Here is what it looks like in freeview:
> 
> Original surface overlay (label is outlined in green)
> 
> [IMAGE]
> 
> The label made into a surface overlay (same  as the one shown in green
> above):
> 
> [IMAGE]
> 
> But this is the output: all zeros even though there was data within the
> mask.
> 
> [IMAGE]
> 
>  
> 
> Help!
> 
> Sara A. Sims
> 
>  
> 
> 
>


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[Freesurfer] help

[Asim Hassan]

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Good afternoon,


I would like to know is there a way to run recon-all on subjects in which 
manual edits have been done on the brainmask.mgz files?

Or at least incorporate manually edited brainmask files into the recon-all 
process?


Thanks!



Asim Hassan
Research Technician II
Division of Pediatric Neurology
University of Texas Southwestern Medical Center



UT Southwestern


Medical Center



The future of medicine, today.

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Re: [Freesurfer] help

[Bruce Fischl]

Hi Asim

if you edited the brainmask in recon-mode in freeview the edits will be 
detected and retained.


cheers
Bruce
On Mon, 14 Oct 2019, Asim Hassan wrote:



External Email - Use Caution

Good afternoon,


I would like to know is there a way to run recon-all on subjects in which
manual edits have been done on the brainmask.mgz files?

Or at least incorporate manually edited brainmask files into the recon-all
process?


Thanks!




Asim Hassan
Research Technician II
Division of Pediatric Neurology
University of Texas Southwestern Medical Center



UT Southwestern

Medical Center

The future of medicine, today.


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Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels

[Bronwyn Overs]

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Hi Kersten, 

That would be very helpful thank you. What email address should I designate as 
the recipient when using Freesurfer FileDrop? 



Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


[ http://neura.edu.au/ | neura.edu.au  ] 



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From: "Kersten Diers, DZNE"  
To: "Freesurfer support list"  
Sent: Wednesday, October 2, 2019 4:21:32 PM 
Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster 
labels 



External Email - Use Caution 


Hi Bronwyn, 

thanks for the update and additional info. 

I have to say that I have no very good clue at the moment. 

Could you maybe upload an examplary file to the Freesurfer FileDrop at [ 
https://gate.nmr.mgh.harvard.edu/filedrop2/ | 
https://gate.nmr.mgh.harvard.edu/filedrop2/ ] so that we can take a closer 
look? 

Best regards, 

Kersten 


On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote: 




External Email - Use Caution 


Hi Kersten, 

Thank you for your detailed reply and sorry for this delayed response. 

Yes the top row in my figure (attached again) was produced by using the 
'--olab' argument with the 'mri_surfcluster' command and then loading each 
cluster from a different label file. I attempted to follow your suggestion and 
adjust the label 'threshold' in Freeview to minimum value in my significance 
map (-5), but this did not display the missing regions - the surface remained 
the same as row 1 of the attached figure. 

To provide you with a little more detail about my method - am using 
'mri_surfcluster' with the '--olab' argument to derive all of my significant 
clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each 
label files (from the 'mri_surfcluster' command) back onto the images for each 
of my individual subjects, and then generate subject level stats for each 
cluster using 'mris_anatomical_stats'. At the moment I am concerned that the 
subject level stats I have derived from my label files do not accurately 
represent each significant cluster in totality as regions appear to be missing 
even when i adjust the minimum threshold. As an alternative, when using 
'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments 
for '--olab', and still perform my 'mri_label2label' and 
'mris_anatomical_stats' steps? 



Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


[ http://neura.edu.au/ | neura.edu.au  ] 



[ https://twitter.com/neuraustralia | Twitter ] | [ 
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ 
http://www.neura.edu.au/help-research/subscribe | Subscribe ] 




From: "Kersten Diers, DZNE"  
To: "Freesurfer support list"  
Sent: Thursday, September 5, 2019 2:13:50 AM 
Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster 
labels 



External Email - Use Caution 


Hi, 

I suppose what we are seeing in the top row of your figure are Freesurfer 
labels, right? I.e. you probably used the '--olab' argument with the 
'mri_surfcluster' command, and are loading each cluster from a different label 
file? 

If my speculation is correct, then what you observe could be due to the 
'threshold' setting in freeview, i.e. this little box just below the label box 
in the left part of the GUI. 

This threshold is by default set to zero, but lowering it to some sufficiently 
negative value (i.e. the minimum value in the 'sig' map) should also display 
those regions that seem to be missing at the moment. 

At least this is what I observed when I tried to reproduce your observation, 
i.e. I could create (and reverse by setting another threshold) similar 
'cut-outs' in the cluster maps. 

In addition, you could also load the ouput files that are produced by the 
'--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I 
would guess that they don't show this pattern of missing areas. 

Hope this helps, 

Kersten 


On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote: 

BQ_BEGIN


External Email - Use Caution 


Dear Freesurfer mailing list, 

I am trying to get to the bottom of a discrepancy between two surface based 
images generated from the output of an LME analysis. The surfaces in row 1 of 
the attached image were generated by loading the four FDR significant clusters 
that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the 
attached image were generated by loading the significance map generated for the 
same fixed effect (saved from the LME), and

Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 21

[Juan Rivas]

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Dear Juan Eugenio, thanks for your answer. I tried to do with the corrected
images and wit the raw ones (before the correction), and I got the same
error. Then I tried with two patients more and happened the same. I don´t
know if it is due to the dev version we used, because the first time it
worked very well.
Best regards,
JC.

El dom., 13 oct. 2019 a las 12:01, 
escribió:

> Send Freesurfer mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
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> Today's Topics:
>
>1. HippoAmyg (Juan Rivas)
>2. Learning dti processing tutorial (Renew Andrade)
>3. Re: HippoAmyg (Iglesias Gonzalez, Juan E.)
>
>
> --
>
> Message: 1
> Date: Sat, 12 Oct 2019 16:02:28 -0400
> From: Juan Rivas 
> Subject: [Freesurfer] HippoAmyg
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
>  k+yph1ddvpw4o67qehmxfhvpem7gqob...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> *Hi, I runned the reconall of my images with FS60 with this command:*
>
> *shiraz[0]:NIFTI$ recon-all -i
>
> /autofs/cluster/neuromod/rivas/imagenes/NIFTI/sub-esq-02-en/anat/sub-esq-02-en_T1w.nii.gz
> -s /autofs/cluster/neuromod/rivas/subject-esq-02-en. There were no errors.*
>
> *Then I runned recon for hippocampus and amygdala with fsdev on Thu Aug 22
> 15:36:32 , with this command:*
>
> *segmentHA_T1.sh*
>
> *There were no errors. Then I identified and corrected manually the errors
> on the FS60 images.*
>
> *Then I run recon-all on fs60 without to touch hippo-amyg.*
>
> *Now, I am trying to make the hippo-amyg correction with this command:*
>
> *segmentHA_T1.sh on fsdev, and I got this error:*
>
>
>
> [shiraz:FS] (nmr-dev-env) segmentHA_T1.sh test1
>
> #
>
> #@# Hippocampal Subfields processing (T1) left Fri Oct 11 17:20:27 EDT 2019
>
> /usr/bin/time -o /dev/stdout
>
> @#@FSTIME 2019:10:11:17:20:27 run_segmentSubjectT1_autoEstimateAlveusML.sh
> N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 1.23
> 1.35 1.67
>
> run_segmentSubjectT1_autoEstimateAlveusML.sh
> /usr/local/freesurfer/dev/MCRv84/ test1 /cluster/neuromod/rivas/imagenes/FS
> 0.
> /usr/local/freesurfer/dev/average/HippoSF/atlas/AtlasMesh.gz
> /usr/local/freesurfer/dev/average/HippoSF/atlas/AtlasDump.mgz
> /usr/local/freesurfer/dev/average/HippoSF/atlas/compressionLookupTable.txt
> 0.05 left L-BFGS v21 /usr/local/freesurfer/dev/bin/ 0
>
> --
>
> Setting up environment variables
>
> ---
>
> LD_LIBRARY_PATH is
>
> .:/lib64:/usr/local/freesurfer/dev/MCRv84//runtime/glnxa64:/usr/local/freesurfer/dev/MCRv84//bin/glnxa64:/usr/local/freesurfer/dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::
>
> Registering imageDump.mgz to hippocampal mask from ASEG
>
> $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
>
>
>
> --mov: Using imageDump.mgz as movable/source volume.
>
> --dst: Using
>
> /cluster/neuromod/rivas/imagenes/FS/test1/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz
> as target volume.
>
> --lta: Output transform as trash.lta .
>
> --mapmovhdr: Will save header adjusted movable as
> imageDump_coregistered.mgz !
>
> --sat: Using saturation 50 in M-estimator!
>
>
>
> reading source 'imageDump.mgz'...
>
> reading target
>
> '/cluster/neuromod/rivas/imagenes/FS/test1/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz'...
>
>
>
> Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
>
>Type Source : 0  Type Target : 3  ensure both FLOAT (3)
>
>Reordering axes in mov to better fit dst... ( -1 3 -2 )
>
>  Determinant after swap : 0.015625
>
>Mov: (0.25, 0.25, 0.25)mm  and dim (131, 99, 241)
>
>Dst: (1, 1, 1)mm  and dim (37, 33, 61)
>
>Asserting both images: 1mm isotropic
>
> - reslicing Mov ...
>
>-- changing data type from 0 to 3 (noscale = 0)...
>
>-- Original : (0.25, 0.25, 0.25)mm and (131, 99, 241) voxels.
>
>-- Resampled: (1, 1, 1)mm and (37, 33, 61) voxels.
>
>-- Reslicing using cubic bspline
>
> MRItoBSpline degree 3
>
> - no Dst reslice necessary
>
>
>
>
>
>  Registration::computeMultiresRegistration
>
>- computing centroids
>
>- computing initial transform
>
>  -- using translation info
>
>- Get Gaussian Pyramid Limits ( min size: 16 max size: -1 )
>
>- Build Gaussian Pyra

Re: [Freesurfer] FS-FAST: cluster size from 1st level analysis

[Greve, Douglas N.,Ph.D.]

Sorry for the delay ...

First, run selxavg3-sess with -fwhm ( you might need to delete the 
bold/analysis folder to get it to re-run).

cd session/bold/analyis
There will be a filed called fwhm.dat. Look in that. Depending upon how much 
you smoothed it might be something like 10.395. This is the FWHM in mm. Next, 
you can run something like the following command

mri_surfcluster --in contrast/sig.nii.gz --hemi lh --csd 
$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/thTT/mc-z.cdf
 --mask mask.nii.gz --sum contrast.sum.dat --oannot ./lh.contrast.annot --thmin 
T --sign abs --subject fsaverage --cwpvalthresh .05

Note that the subject must be fsaverage because the tables were computed with 
fsaverage. Above, fwhmXX would be fwhm11 (because the FWHM is 10.395, but round 
up to 11). TT refers to the cluster forming threshold (eg, p<.001 would be 30), 
and so --thmin T would be 3. "abs" in the path to the CSD file indicates that 
you want to use an unsigned (absolute) value; you can also use pos and neg. 
--cwpvalthresh .05 means to filter out any clusters that are not significant at 
p=0.05. The cluster table will be in contrast.sum.dat

doug


On 10/3/2019 7:52 AM, Keri Woods wrote:

External Email - Use Caution

Hi

From the 1st level analysis of an fMRI study I'm trying to extract the size of 
the clusters of activation from each subject, but don't know how to go about 
this. I know that for the group analysis you can get the cluster sizes from the 
output from mri_glm-sim. Is there a way to run the multiple comparison 
correction on the first level analysis in order to get this table? Or is there 
another way of getting the cluster sizes?

Any help would be much appreciated.

Thank you,
Keri



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