Re: [Freesurfer] Is it possible to "fill in" the region delimited by an ROI label?

External Email - Use Caution Hello Dr. Greve, Thank you for the response. I have extensively searched through the options available to me in freeview, but I could not find any sort of checkbox that turns off outline mode. Here is what I see, having selected the label file:

Re: [Freesurfer] Issue with MATLAB 2012 runtime download

External Email - Use Caution It worked! Thank you! On Wed, Mar 18, 2020 at 10:07 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Please try: > > sudo curl " >

Re: [Freesurfer] SPM Volumes on FSAVERAGE surfaces

External Email - Use Caution I could do that, but for consistency with the some other results, it would be nice if I could get them on FSAVERAGE instead. Are there any good ways to do that other than registering an MNI brain to the fsaverage T1 and carrying the statistical image

Re: [Freesurfer] selxavg3-sess not working

Hi Doug Thanks for your reply. Unfortunately I am still having problem. It’s so odd, because it has never happened with my other subjects before. I attached the log files and I appreciate if you could please take a look. command: selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh On

Re: [Freesurfer] extracting values of each voxel within an ROI

Hi Doug Thank you very much for your reply. I am doing these analysis in each subject’s self space, and my ROI is a handmade cortical label in ascci format. In this case, would the indices be the vertex Id in the label file? also, instead of f=MRIread('f.nii.gz’); can I use “sig.nii.gz” to get

Re: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).

External Email - Use Caution Hello Douglas, If I do ls $SUBJECTS_DIR/ben, the T1 image will show up as predicted. However if I tried to recon-all, the error will pop up. Many Thanks Peng Liu, PhD Candidate Institut für Kognitive

Re: [Freesurfer] Skull-stripped brain for non-T1 image

First register the T2/FLAIR to the anatomical bbregister --mov T2.mgz --T2 --reg reg.T2.lta --subject subject Then map it to the orig space mri_vol2vol --mov T2.mgz --reg.T2.lta --fstarg --o T2-in-orig.mgz then Apply the mask mri_mask T2-in-orig.mgz brain.mgz T2-in-orig-masked.mgz On 3/20/2020

Re: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).

What is your SUBJECTS_DIR set to? What do you get if you ls $SUBJECTS_DIR/ben On 3/20/2020 9:48 AM, Peng Liu wrote: External Email - Use Caution Hi Andrew, Thank you for your reply. I have tried this command you sent me rm -rf $SUBJECTS_DIR/ben It indeed deleted the ben folder

Re: [Freesurfer] Is it possible to "fill in" the region delimited by an ROI label?

There should be a check box in the label config area to turn off outline mode On 3/19/2020 1:11 PM, Mohammad Rashid wrote: External Email - Use Caution Hi all, I'm able to load in a yellow outline for the entorhinal region by loading a file named ?h.entorhinal_exvivo.label as a

Re: [Freesurfer] Flip left-right orientation command

Have you tried using LAS ? On 3/19/2020 12:48 PM, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Dear Douglas, In these emails I asked to you how to flip the left-right orientation of an image in PIL orientation and you recommend to me this command mri_convert

Re: [Freesurfer] extracting values of each voxel within an ROI

Do you mean all the voxels separately? I don't think I have anything, but you can do it in matlab with something like seg = MRIread('seg.nii.gz'); indices= find(seg.vol == IndexOfYourROI); f = MRIread('f.nii.gz'); fmat = fast_vol2mat(f); froi = fmat(:,indices); this assumes taht f.nii.gz and

Re: [Freesurfer] SPM Volumes on FSAVERAGE surfaces

Try running recon-all on the mni152 On 3/18/2020 5:05 PM, Ryne Nichols wrote: External Email - Use Caution All, I'm having trouble getting good surface projections of SPM results. My SPM results come from SPM normalization -- which should be MNI152 space. I'm confused because

Re: [Freesurfer] Failed to load Surface lh.white

You only ran it through -autorecon1, rerun with -all or with -autorecon2 -autorecon3 to generate all  the files On 3/17/2020 12:31 PM, Alexander Barnett wrote: External Email - Use Caution Hello FreeSurfer Developers, I am trying to inspect the white matter gray matter surface to

Re: [Freesurfer] mri_glmfit and mri_glmfit-sim

Did you download the patch? See the " If You're Not at an Organized Course" part of this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 3/17/2020 11:31 AM, Varun Chandran wrote: External Email - Use Caution Dear FS experts, I am trying

Re: [Freesurfer] cortical area and volume calculation method

The area is just the sum of the area of the triangles in an ROI. For volume, we use Anderson Winkler's method of dividing each obliquely truncated trilateral pyramid into three tetrahedra. I don't know of a reference, but I've cc'ed Anderson. On 3/17/2020 11:06 AM, Ting Li wrote: >

Re: [Freesurfer] training set

Try the tutorial slides https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI It does not go into a lot of detail, but it will give you the relevant lectures On 3/17/2020 8:54 AM, javier quilis wrote: External Email - Use Caution Hello everyone, I'm trying to do a

[Freesurfer] Skull-stripped brain for non-T1 image

External Email - Use Caution Hi everyone, Suppose I have run Freesurfer with respect to a subject using the T1 image, and I have gotten the skull-stripped brain image (brain.mgz) in the /mir directory. Now I have a non-T1 image of the same subject, say, the (T2)FLAIR series, and

Re: [Freesurfer] selxavg3-sess not working

oh, sorry, I misread your earlier email. The -force in selxavg3-sess only applies to the post processing. If  you want to redo the preprocessing, then run preproc-sess -force On 3/13/2020 7:28 PM, Nasiriavanaki, Zahra wrote: Hi Doug Thanks for your reply. Yes, I did. I run the command from

Re: [Freesurfer] Troubleshooting fix topology lh stall

also, if you run defect-seg, it will create a segmentation of the defects which you can visualize in the volume. Run defect-seg with --help for more info On 3/13/2020 8:45 PM, Bruce Fischl wrote: Hi Ricky how did you try to load the defect_labels? The end of the recon-all.log file lists a

Re: [Freesurfer] Permutation simulation produces unexpected results

The situation is complicated. First, you should run with --cwp 1 to get a list of all clusters. it maybe that a cluster is just barely out of threshold and so does not show up in the list. When you change the threshold you, you change the probability curve and obviously the size of the

Re: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).

External Email - Use Caution Hi Andrew, Thank you for your reply. I have tried this command you sent me rm -rf $SUBJECTS_DIR/ben It indeed deleted the ben folder under the subject directory, but when I try to run recon-all for this participant under another name, it still

Re: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).

Hi Peng, Are you sure you’re deleting the subject folder from within the SUBJECTS_DIR? rm -rf $SUBJECTS_DIR/ben Should clear the issue. best Andrew From: on behalf of Peng Liu Reply-To: FS Help Date: Friday, March 20, 2020 at 6:39 AM To: FS Help Subject: [Freesurfer] Error with

[Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).

External Email - Use Caution Dear all, I am trying to run recon-all command for a subject ben. Before I perform this command, I have exported SUBJECTS_DIR to a folder with only T1 data for this subject ben in it. However after I entered the command "recon-all -s ben -i T1.nii