Re: [Freesurfer] Surface-based analysis of tfMRI

Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the image has a proper baseline so that the registration will work. On 10/22/18 11:14

Re: [Freesurfer] Surface-based analysis of tfMRI

External Email - Use Caution Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume? On Mon, 22 Oct

[Freesurfer] Is the cortical thickness calculated using Hausdorff distance in FreeSurfer?

External Email - Use Caution Dear FS experts: I'm doing a project about the changes of cortical thickness after sleep deprivation. I know that cortical thickness is calculated as the closest distance from the gray/white boundary to the gray/CSF boundary at each vertex. Is

Re: [Freesurfer] resampling data onto cortical surface

I would just do mri_vol2vol --i vin.nii --regheader --targ orig.mgz --o vout.mgz On 10/22/2018 05:52 PM, GREGORY R KIRK wrote: > > External Email - Use Caution > > thanks Doug, one more thing to make sure I get it correct. > > > If I have a volume of quantitative MR volumes in the native

Re: [Freesurfer] resampling data onto cortical surface

External Email - Use Caution thanks Doug, one more thing to make sure I get it correct. If I have a volume of quantitative MR volumes in the native space of the T1 and I want them to be in registration with the freesurfer space of this subject I woiuld mri_convert -it nii

Re: [Freesurfer] Surface-based analysis of tfMRI

If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm. On 10/22/2018 04:08 PM, Zhi Li wrote: > > External Email - Use Caution > >

[Freesurfer] Surface-based analysis of tfMRI

External Email - Use Caution Hi FreeSurfer Experts, I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with

Re: [Freesurfer] Myelinated cortical thickness ratio map

External Email - Use Caution Regression would be better than division. Matt. From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Damien MARIE mailto:damien.ma...@unige.ch>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday,

Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

yes, they are surfaces. You need to specify -f on the command line before listing the surfaces you want to load On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution I tried. I cannot open them. They are not .mgz files, they are binary files.I will

Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

External Email - Use Caution I tried. I cannot open them. They are not .mgz files, they are binary files. I will try though, and see what is happening. Thank you, Rosalia El lun., 22 oct. 2018 21:49, Bruce Fischl escribió: > with freeview > On Mon, 22 Oct 2018, Rosalia Dacosta

Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

with freeview On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Hi Bruce, I cannot examine those files with gedit. Could you tell me how to open them? Thank you, Rosalia On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl wrote: Hi Lisa

Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

External Email - Use Caution Hi Bruce, I cannot examine those files with gedit. Could you tell me how to open them? Thank you, Rosalia On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl wrote: > Hi Lisa > > no, likely you have to identify and correct the source of the giant >

Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

External Email - Use Caution HI Bruce, Thank you for the quick reply! Are there online tutorials that could show me how to implement your suggestions? Best, -Lisa -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

Hi Lisa no, likely you have to identify and correct the source of the giant defect, typically be either fixing the skull stripping, or editing the wm.mgz or adding control points cheers Bruce On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote: External Email - Use Caution Hi

Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

External Email - Use Caution Hi all, I have a stroke brain with a large lesion that runs into this same problem. Is there a way to push the process along? No white matter segmentations are created to try and edit the surface. Best, -Lisa Krishnamurthy -Original

Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

Hi Rosaila usually when you have a defect that large (>30,000) vertices, which is about 1/4 of the total surface more or less, something is dramatically wrong and it is not worth waiting for it to finish (it might take days or weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces

[Freesurfer] Stuck in "CORRECTING DEFECT"

External Email - Use Caution Dear FreeSurfer team, I Have run -autorecon1 in my sample and the report.log was "finished without errors" Now, running recon-all -all I have seen that a participant is stuck in CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more

[Freesurfer] postdoctoral research opportunity

FYI -- Forwarded message -- Date: Mon, 22 Oct 2018 12:16:59 -0700 From: Rahul Desikan To: Bruce Fischl Subject: one more favor External Email - Use Caution One more favor Bruce. If possible could you please post this on the FS/FSL lists? Many thanks! Best,

Re: [Freesurfer] GE data issue

Did you look at the nifti volumes? Are they 2 sets of diffusion-weighted images? If so, you can concatenate them into 1 volume with mri_concat. You will also have to concatenate the text files that contain the b-values of the 2 scans, and those that contain the gradient directions of the 2

[Freesurfer] GE data issue

External Email - Use Caution Dear sir/madam, I try to use TRACULSR to analysis DTI data of GE machine. But when I transfer origin data to nii, I found 2 nii file producted per sample. Can I use these data to run TRACULAR、 If yes, how can I combine 2 nii file? I

Re: [Freesurfer] resampling data onto cortical surface

Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). btw, if you have multi echo data, you are probably measuring R2*, not R1. On 10/22/2018 12:55 PM, GREGORY R KIRK wrote: > > External Email - Use Caution > > > I have R1 values that I want to resample onto

[Freesurfer] resampling data onto cortical surface

External Email - Use Caution I have R1 values that I want to resample onto the cortical surface. The R1 values were computed from a multi echo T1 sequence that was also used to create the T1 weighted image that was used in recon-all to produce the cortical surface

[Freesurfer] (no subject)

External Email - Use Caution Dear freesurfer, I have some question about GE date (have 2 run) to run TRACULAR. How can I get some answers? Sent from Mail for Windows 10 ___ Freesurfer mailing list

[Freesurfer] Myelinated cortical thickness ratio map

External Email - Use Caution Dear experts, I am working with R1 maps that I project on the surface. The goal is to look at intra-cortical myelin. I detect interesting effects between two groups. Now I would like to compute myelinated cortical thickness ratio maps, in order to

Re: [Freesurfer] Which command generates the lh.area.pial.fsaverage.mgh file?

External Email - Use Caution Nevermind, I found in the source code of recon-all (line 180) that you have to specify the measure as '-measure area.pial' instead of '-measure area' in this case. Sorry for the noise. Tim > On October 22, 2018 at 11:23 AM ts...@rcmd.org wrote:

[Freesurfer] Which command generates the lh.area.pial.fsaverage.mgh file?

External Email - Use Caution Dear FreeSurfer experts, I would like to know how to (re-)generate the files 'lh.area.pial.fsaverage.mgh' and 'rh.area.pial.fsaverage.mgh' for a subject (in the surf/ dir). I have tried the following: 1.) ensured that the source files, lh.area.pial