[Freesurfer] Problem of VolumeRoiCorticalThickness

Hi all, I want to extract cortical thickness for a ROI (dlpfc) which was defined in volume space. I search it in Freesurfer Wiki and find the description in website (http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness). But, in the second, it said it need an T1 volume (average

Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )

Hi Elia - It looks like this file didn't get created: /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz The command that was supposed to create it was epidewarp.fsl. You can find the command line that begins with "epidewarp.fsl" in the log file that you sent m

[Freesurfer] Questions about cluster-wise correction

Hi, all, I have two quesiotns about clusterwise correction for multiple comparsion. I run 2 corrections for one same result,and commands are as follows: a. mri_glmfit-sim --glmdir g2v0.weight --cache 2.0 abs --cwpvalthresh .05 --2spaces b. mri_glmfit-sim --glmdir g2v0.weight --cache 2.0 pos --cw

Re: [Freesurfer] Problem of VolumeRoiCorticalThickness

Hi Wang what volume space is it defined in? Generally you can use mri_label2label with the --paint option to sample a label onto a surface. cheers Bruce On Sun, 15 Jun 2014, wangkangcheng_gmail wrote: Hi all,   I want to extract cortical thickness for a ROI (dlpfc) which was defined in vol

[Freesurfer] subcortical segment NIFTI files

Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.

Re: [Freesurfer] subcortical segment NIFTI files

Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce > On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" wrote: > > Dear all, > > While it is possible to obtain NIfTI files for cortical parcellation using > mri_annotation2label, I am

Re: [Freesurfer] subcortical segment NIFTI files

Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use fo

Re: [Freesurfer] subcortical segment NIFTI files

mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce > On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" wrote: > > Hi Bruce, > > Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very >

Re: [Freesurfer] subcortical segment NIFTI files

Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mg

[Freesurfer] Extract the mean cortical thickness of each significant clusters

Dear Freesurfer Experts, I would like the mean thickness measures of each clusters i found in qdec from both control and patient group. I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group. I found 30 different significant clusters afte

[Freesurfer] Extract the mean cortical thickness of each significant clusters

Dear Freesurfer Experts, Please ignore the previous email. I would like the mean thickness measures of each clusters, survived after multiple comparison correction, in qdec. I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group. I fou

[Freesurfer] reg.1mm.mni152.dat

Dear all, While there is the file ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat, there is no such file as: ${FREESURFER_HOME}/subjects/fsaverage/mri/reg.1mm.mni152.dat or ${FREESURFER_HOME}/subjects/fsaverage/mri/transforms/reg.1mm.mni152.dat ? I am wondering how we can

Re: [Freesurfer] Problem of VolumeRoiCorticalThickness

Dear Bruce, Now, I change the standard atlas to avg152T1.nii.gz which was included in the FSL and make a mask of superior frontal gyrus (Harvard-Oxford Cortical Structural Atlas). I can map the ROI-mask to the fsaverage surface to create an fsaverage-ROI surface overlay. But when I map one sub