Re: [Freesurfer] Voxel to Surface Coordinates

. -- what are MNI surface coords? On 5/14/19 5:30 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > Hello, > > We have an anatomical atlas that we have incorporated in the > FreeSurfer pipeline. Is it possible

[Freesurfer] Voxel to Surface Coordinates

External Email - Use Caution Hello, We have an anatomical atlas that we have incorporated in the FreeSurfer pipeline. Is it possible to convert this voxel based atlas into MNI152 surface coordinates? Any suggestions or comments would be greatly appreciated. Thank you, Da-Yea -

[Freesurfer] Partial volume correction for aseg.mgz files

External Email - Use Caution Hello, I'm trying to extract regions (mri_extract_label) of interest from the aseg.mgz files and compare them to our manual segmentations. I've warped these ROI masks onto our native space. I've noticed on the forum that there were mentions of discr

[Freesurfer] mri_binarize --replace

External Email - Use Caution Hello, I have a set of binary mask files that I'm trying to assign different values to. Currently I'm doing: mri_binarize --i sub001.nii.gz --o final_sub001.nii.gz --replace -117 2 mri_binarize --I sub002.nii.gz --o final_sub002.nii.gz --replace -128

[Freesurfer] mri_convert --in_center

External Email - Use Caution Hello, Is it possible to change the origin of the aseg.mgz file? I tried mri_convert --in_center -117 -219 145 aseg.mgz new_aseg.img. When I opened the new_aseg.img file the origin seems to be at 0 -127 0. Any suggestions would be greatly appreciate

[Freesurfer] Calculating volume using pial files

External Email - Use Caution Hello, I'm trying to calculate the volume using pial files. Is there a way to convert ?h.pial files into nii formats? Or is there a command to calculate the volume? Thank you so much in advance for your help. Best regards, Da-Yea Song -

Re: [Freesurfer] Extracting both the GM and WM ROIs

wmparc.mgz file? On 12/11/2018 05:16 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > Hello, > > I've been trying to extract ROIs directly from the Desikan atlas by > using the mri_annotation2label and the aparc.annot files from the > fsaverage folder.

[Freesurfer] Extracting both the GM and WM ROIs

External Email - Use Caution Hello, I've been trying to extract ROIs directly from the Desikan atlas by using the mri_annotation2label and the aparc.annot files from the fsaverage folder. I noticed that this pulls out the grey matter portion for these regions but was wondering i

Re: [Freesurfer] Extracting ROI from atlases

] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote: >External Email - Use Caution &g

Re: [Freesurfer] Extracting ROI from atlases

urfer] Extracting ROI from atlases the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote: >External Email - Use Caution > > I really appreciate the quick reply back Bruce! > > I tried the following: mri_binaraize --i lh.apar

Re: [Freesurfer] Extracting ROI from atlases

bject: Re: [Freesurfer] Extracting ROI from atlases $FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot On Fri, 7 Dec 2018, Song, Da-Yea wrote: >External Email - Use Caution > > Could you please direct me on where I could find the fsaverage annot file > for the Desikan

Re: [Freesurfer] Extracting ROI from atlases

Of Bruce Fischl Sent: Friday, December 07, 2018 3:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases yes, use the fsaverage annot file. That is essentially what you want cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote: >External Email -

Re: [Freesurfer] Extracting ROI from atlases

; Sent: Thursday, December 06, 2018 11:50 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Extracting ROI from atlases > > You can use > mri_binarize --i aparc+aseg.mgz --match 1028 --o > ctx-lh-superiorfrontal.nii.gz See  > $FREESURFER_HOME/FreeSurferColorLUT

Re: [Freesurfer] Extracting ROI from atlases

] Extracting ROI from atlases You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See  $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use On 12/04/2018 12:51 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > H

[Freesurfer] Extracting ROI from atlases

External Email - Use Caution Hello, Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats? Thank you so much in advance for your time. Best, Da-Yea -- Disclaimer: The materials

Re: [Freesurfer] CerebralWhiteMatterVol {Disarmed}

...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, November 20, 2018 6:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] CerebralWhiteMatterVol No, it does not. On 11/20/18 3:54 PM, Song, Da-Yea wrote: External Email - Use Caution Hello, Does the

[Freesurfer] CerebralWhiteMatterVol

External Email - Use Caution Hello, Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum? Thank you so much in advance for your help! Best, Da-yea -- Disclaimer: The materials in this

Re: [Freesurfer] aseg.stats calculations {Disarmed}

20, 2018 1:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aseg.stats calculations On 11/20/18 1:37 PM, Song, Da-Yea wrote: External Email - Use Caution Hello, I had a question regarding the aseg.stats and was hoping to get some help. 1. How is the TotalGray

[Freesurfer] aseg.stats calculations

External Email - Use Caution Hello, I had a question regarding the aseg.stats and was hoping to get some help. 1. How is the TotalGray calculated? On the wiki page it mentioned that it is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried calculating th

[Freesurfer] recon-all error

External Email - Use Caution Hello, I'm running some subjects through recon-all but have noticed that some error out (terminate the job) within seconds of starting. Any suggestions would be really appreciated. Here is the recon-all.cmd error message: #--

[Freesurfer] Unknown Region_Stats

External Email - Use Caution Hello, I read on the website FAQ that "if you use the values in the ?h.aparac.stats, it already factors out the 'unknown' region, so you don't have to do it yourself". Is there a way to view stats (ex. thickness, area, volume) for these unknown regi

[Freesurfer] Stats Error

External Email - Use Caution Hello, I'm extracting some stats from recon-all but noticed that it would stop running in the middle (error message: end: Not in while/foreach) . Any suggestions on how I could solve this problem would be greatly appreciated! Thank you so much in ad

Re: [Freesurfer] MRIread error

du Subject: Re: [Freesurfer] MRIread error Check permissions first. Look at the size of the file. Is it much smaller than other rh.white files in other subjects? Have you run out of disk space? On 08/29/2018 04:37 PM, Song, Da-Yea wrote: > > External Email - Use Caution > >

[Freesurfer] MRIread error

External Email - Use Caution Hi everyone, I'm trying to pre-process subjects through the pipeline but keep getting a handful of subjects that error out within seconds of running them. The error message I get is: MRISread(/subjects/002_1006/surf/rh.white):could not open file When