Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

External Email - Use Caution Hi Bruce, this did not change anything. But I tried the process of mris_ca_train, mris_ca_label with lh.oasis.chubs.annot and this worked fine. A closer look to my source annot file from mris_seg2annot showed that the label 'unknown' is missing. How c

Re: [Freesurfer] 回复： How to extract cortical features of a ROI

Oh, the vertex indices of the label are stored in the label file. You can use the. To index into the thickness vector Cheers Bruce > On Mar 5, 2019, at 10:09 PM, 310913949 <310913...@qq.com> wrote: > > External Email - Use Caution > > Hi Bruce， >The ‘mris_anatomical_stats‘’

[Freesurfer] ?????? How to extract cortical features of a ROI

External Email - Use Caution Hi Bruce?? The ??mris_anatomical_stats and 'mri_segstats?? command line just output mean thickness of ROI, but I want to know cortical thickness for each vertex in the ROI. So I think the key is to find the coordination of each vertex in th

[Freesurfer] Postdoc positions at Washington University

External Email - Use Caution ** Apologies for cross-postings ** The research group of Dr. Sotiras (www.asotiras.com), a part of the Electronic Radiology Lab at Washington University in St. Louis ( https://wustl.edu), is currently seeking a highly motivated postdoctoral research as

[Freesurfer] HCP Course 2019: Get ready for more data, and a new way of getting it

External Email - Use Caution *More HCP data are comingand will be released in a new way.will you be ready? * This spring, the first data from the Lifespan Human Connectome Projects - (HCP) Development (healthy subjects ages 5-21) and HCP Aging (ages 36-100+) will be public

Re: [Freesurfer] extracting cortical parcellation

Hi Atena yes, mri_annotation2label should work, although it really depends on what you want to do next cheers Bruce On Wed, 6 Mar 2019, Atena Rezaei wrote: External Email - Use Caution Hello, I am trying to extract the cortical parcellation(atlas) file from freesurfer  wit

[Freesurfer] PETSurfer and thickness data

External Email - Use Caution Dear FS community, I would like to assess how PET tracer uptake is related to thickness changes in AD patients. Is it possible to generate difference maps for both methods and run a GLM? Or would you suggest another approach? Thanks, Boris

[Freesurfer] extracting cortical parcellation

External Email - Use Caution Hello, I am trying to extract the cortical parcellation(atlas) file from freesurfer with all the labels. I found the lh.aparc.annot file in label folder. Should I use mri_annotation2label to create labels? or how can I extract the whole file? Thanks fo

Re: [Freesurfer] Computing LGI using Octave instead of Matlab

External Email - Use Caution Maybe you already know this, but just in case: mris_compute_lgi is a shell script, so you can open it in an editor and check what it does.cat The output of the following command gives a good first impression: cat `which mris_compute_lgi` | grep -

Re: [Freesurfer] Processing MEMPRAGE

Great - thanks for clarifying! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Andre van der Kouwe Sent: Tuesday, March 5, 2019 2:57:13 PM To: Bruce Fischl Cc: Freesurfer support list; Sevinc, Gunes; Lazar, Sara Subject: Re: [Freesurfer] Processing ME

Re: [Freesurfer] Processing MEMPRAGE

Yes, that's correct, it's the smaller RMS file. FreeSurfer will complain if it's supplied with a multi-frame (4 echo) volume i.e. you should get a warning if you use the wrong file. On Tue, 5 Mar 2019, Bruce Fischl wrote: Hi Johann I believe that is the case, but Andre (ccd) can confirm che

[Freesurfer] Computing LGI using Octave instead of Matlab

External Email - Use Caution Hello all, Is there a way to run LGI commands listed below using Octave instead of Matlab? I've read somewhere on the forums of being able to get Freesurfer to use Octave instead of Matlab in FSFAST but I'm not sure if it will work with the commands be

Re: [Freesurfer] Processing MEMPRAGE

Hi Johann I believe that is the case, but Andre (ccd) can confirm cheers Bruce On Tue, 5 Mar 2019, Rusche, Johann wrote: Dear Freesurfers, Reading through the mailing list I understood how to process our nmr MEPRAGEs  and I would like to double-check we are using unpacksdcmdir correctly.

[Freesurfer] Processing MEMPRAGE

Dear Freesurfers, Reading through the mailing list I understood how to process our nmr MEPRAGEs and I would like to double-check we are using unpacksdcmdir correctly. Unpacking with unpacksdcmdir gives me two nifti files, a 4-echo nifti file (92MB) and a 1-echo nifti file (23MB). Am I correct

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

External Email - Use Caution Hi, I am still struggling to examine differences in thickness using the command line stream for my two groups after controlling for age and sex. I get the following error when running the command line: ERROR: matrix is ill-conditioned or badly scal

[Freesurfer] Masks in mri_segstats

External Email - Use Caution Hello Freesurfer experts, I would like to use mri_segstats with two different masks and thresholds, such as: mri_segstats --mask mask1 --maskthresh thresh1 --mask mask2 --maskthresh thresh2 This command can run smoothly with our any error. However, I

Re: [Freesurfer] Should I edit or reject?

Hi Ryan I'm not sure we have much useful advice to give you as it depends a lot on your subject population. Basically we make the decision of whether or not a given dataset is good enough quality to extract biologically meaningful results from. If you are only interested in a bit of the brain

[Freesurfer] Should I edit or reject?

External Email - Use Caution Hi, Although there are many ways to correct for pial, WM, and segmentation defects, it seems common in the literature to forego any edits and simply either accept or reject a subject's FreeSurfer output in order to avoid subjectivity and potential over

Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

Hi Joerg I'm not positive that I understand, but have you tried giving mris_ca_label the switch: mris_ca_label -l $SUBJECTS_DIR/$subject/label/$hemi.cortex.label ... that should remove non-cortical regions from your output annot cheers Bruce On Tue, 5 Mar 2019, Jörg Stadler wrote:

Re: [Freesurfer] Surface Misplacement

Hi Banu can you send us an image to show us what you mean? cheers Bruce On Tue, 5 Mar 2019, Banu Femir wrote: External Email - Use Caution Hi, I've a problem about surface placement. For my PhD thesis, I've been analyzing T1 images of 103  AD, MCI and SCI subjects. I'm usin

Re: [Freesurfer] How to extract cortical features of a ROI

Hi Kan you can give the surface-based label to mris_anatomical_stats and it will constrain it's calculations to the label (where it makes sense): mris_anatomical_stats -l ... you can probably do it with mri_segstats too - Doug will know cheers Bruce On Tue, 5 Mar 2019, 310913949 wrote:

Re: [Freesurfer] mri_vol2surf sample inside and outside of pial

yes, although note that neither one is guaranteed to be "inside" or "outside" at that distance (it might reenter the surface in the outwards normal direction, or leave the surface in the inwards direction) cheers Bruce On Tue, 5 Mar 2019, Michael Jordan wrote: External Email - Use

[Freesurfer] Surface Misplacement

External Email - Use Caution Hi, I've a problem about surface placement. For my PhD thesis, I've been analyzing T1 images of 103 AD, MCI and SCI subjects. I'm using FS 6.0 stable version on Linux. Some of my data, especially AD data have a surface problem. White matter includes

Re: [Freesurfer] How to extract cortical features of a ROI

External Email - Use Caution Hi bruce?? I still have some questions about extracting cortical features of a ROI. I used the mri_label2label to sample the volumetric label to the surface of the subject. But I dont know how to do next, as i found that the RAS coordinates do no

[Freesurfer] mri_vol2surf sample inside and outside of pial

External Email - Use Caution Hi, I have a short question concerning the mri_vol2surf command. Do the following parameters of the command return the maximum volume value (for each vertex) which occurs between 10 mm outside and 10 mm inside the pial surface (along normal vector)?