Re: [Freesurfer] Turning Significant Cluster (sig.cluster.summary or sig.mgh) into binary .nii ROI

2022-03-27 Thread Douglas N. Greve 
Are you trying to create a volume-based binary mask or a surface-based 
mask? From the commands below, it looks like surface (but why would you 
need it to be in nii?). In the surface case, you can just

mri_binarize --i ocn.mgh --match clusterno --o clusterno.mask.nii
where "ocn" is the ocn file created by mri_glmfit-sim and clusterno is 
the number of the cluster



On 3/16/2022 3:00 PM, Emily Popa wrote:


External Email - Use Caution

Hello, I am just following up on my previous question. To put it more 
shortly (I apologize for making the question so long before), I am 
just searching for a way to convert a significant cluster from a group 
analysis into a binary .nii mask so I can use the mask (after some 
registration steps) to perform ASL analysis in that specific ROI for 
the same subjects (in FSL).


Best,

Emily S. Popa, M.S.

Staff Research Associate II, Neuroimaging

Pacific Brain Health Center | Pacific Neuroscience Institute 
Foundation | Providence Saint John’s Health Center


1301 20^th  St. #250 Santa Monica, CA. 90404

(408) 750-7971 (M)

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*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Emily Popa 


*Date: *Thursday, March 10, 2022 at 2:31 PM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *[Freesurfer] Turning Significant Cluster 
(sig.cluster.summary or sig.mgh) into binary .nii ROI


*External Email - Use Caution *

Hello,

I have been struggling to figure out a way to get the significant 
results of a freesurfer group analysis (just one significant cluster) 
from either the sig.cluster.summary or sig.mgh file into a binarized 
ROI in .nii format. I used mri_glmfit to perform the cortical 
thickness analysis on sMRI data and found the significant cluster only 
in the left hemisphere. I tried to follow some instructions I found on 
the FreeSurfer site, however, at the first step/line below 
(mri_volsynth) the –delta-crsf input was referred to on the site as 
the vertex number, but on the –help documentation, it was specified 
that this input should be: col row slice frame : 0-based. Looking at 
the cluster summary file, for the significant cluster there is a 
maximum vertex, but I am not sure if this is the vertex number I 
should be using.


mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness 
--pdf delta --delta-crsf 5 9 5 1 --o delta.sm00.mgh


mris_fwhm --smooth-only --subject fsaverage --hemi lh --i 
delta.sm00.mgh --niters 10 --o delta.sm10.mgh


mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh

When trying the first line above for mri_volsynth, I get this error: 
Segmentat

Re: [Freesurfer] Turning Significant Cluster (sig.cluster.summary or sig.mgh) into binary .nii ROI

2022-03-16 Thread Emily Popa 
External Email - Use Caution

Hello, I am just following up on my previous question. To put it more shortly 
(I apologize for making the question so long before), I am just searching for a 
way to convert a significant cluster from a group analysis into a binary .nii 
mask so I can use the mask (after some registration steps) to perform ASL 
analysis in that specific ROI for the same subjects (in FSL).

Best,

Emily S. Popa, M.S.
Staff Research Associate II, Neuroimaging
Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | 
Providence Saint John’s Health Center
1301 20th St. #250 Santa Monica, CA. 90404
(408) 750-7971 (M)
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Emily Popa 

Date: Thursday, March 10, 2022 at 2:31 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Turning Significant Cluster (sig.cluster.summary or 
sig.mgh) into binary .nii ROI

External Email - Use Caution
Hello,

I have been struggling to figure out a way to get the significant results of a 
freesurfer group analysis (just one significant cluster) from either the 
sig.cluster.summary or sig.mgh file into a binarized ROI in .nii format. I used 
mri_glmfit to perform the cortical thickness analysis on sMRI data and found 
the significant cluster only in the left hemisphere. I tried to follow some 
instructions I found on the FreeSurfer site, however, at the first step/line 
below (mri_volsynth) the –delta-crsf input was referred to on the site as the 
vertex number, but on the –help documentation, it was specified that this input 
should be: col row slice frame : 0-based. Looking at the cluster summary file, 
for the significant cluster there is a maximum vertex, but I am not sure if 
this is the vertex number I should be using.

mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf delta 
--delta-crsf 5 9 5 1 --o delta.sm00.mgh
mris_fwhm --smooth-only --subject fsaverage --hemi lh --i delta.sm00.mgh 
--niters 10 --o delta.sm10.mgh
mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh

When trying the first line above for mri_volsynth, I get this error: 
Segmentation fault: 11 (so I think my input –deta-crsf is likely wrong). If 
there is a better way to convert this ROI to a mask, please let me know!

To give additional context, I am hoping to get a binary mask of this ROI that I 
can use as a mask for an ASL analysis in FSL (to limit the analysis to this 
ROI). I plan to do this by registering the binary ROI mask to the FSL standard 
group template (by using the transformati

[Freesurfer] Turning Significant Cluster (sig.cluster.summary or sig.mgh) into binary .nii ROI

2022-03-10 Thread Emily Popa 
External Email - Use Caution

Hello,

I have been struggling to figure out a way to get the significant results of a 
freesurfer group analysis (just one significant cluster) from either the 
sig.cluster.summary or sig.mgh file into a binarized ROI in .nii format. I used 
mri_glmfit to perform the cortical thickness analysis on sMRI data and found 
the significant cluster only in the left hemisphere. I tried to follow some 
instructions I found on the FreeSurfer site, however, at the first step/line 
below (mri_volsynth) the –delta-crsf input was referred to on the site as the 
vertex number, but on the –help documentation, it was specified that this input 
should be: col row slice frame : 0-based. Looking at the cluster summary file, 
for the significant cluster there is a maximum vertex, but I am not sure if 
this is the vertex number I should be using.

mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf delta 
--delta-crsf 5 9 5 1 --o delta.sm00.mgh
mris_fwhm --smooth-only --subject fsaverage --hemi lh --i delta.sm00.mgh 
--niters 10 --o delta.sm10.mgh
mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh

When trying the first line above for mri_volsynth, I get this error: 
Segmentation fault: 11 (so I think my input –deta-crsf is likely wrong). If 
there is a better way to convert this ROI to a mask, please let me know!

To give additional context, I am hoping to get a binary mask of this ROI that I 
can use as a mask for an ASL analysis in FSL (to limit the analysis to this 
ROI). I plan to do this by registering the binary ROI mask to the FSL standard 
group template (by using the transformation matrix from registering the 
fsaverage template to FSL’s standard group template first), and then getting 
the ROI mask from FSL’s group template space into native ASL space. If this 
plan sounds reasonable to you, it would also be very helpful to know.

I really appreciate your time and help and look forward to hearing back!



Best,

Emily S. Popa, M.S.
Staff Research Associate II, Neuroimaging
Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | 
Providence Saint John’s Health Center
1301 20th St. #250 Santa Monica, CA. 90404
(408) 750-7971 (M)
[cid3519*image001.jpg@01D7EC78.96AA1AC0]
 [cid3519*image002.jpg@01D7EC78.96AA1AC0] 

  [cid3519*image003.jpg@01D7EC78.96AA1AC0] 

  [cid3519*image004.jpg@01D7EC78.96AA1AC0] 

  [cid3519*image005.jpg@01D7EC78.96AA1AC0] 


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