[Freesurfer] How can I visualize cortical thickness data on a brain template?

External Email - Use Caution Hello FreeSurfer technical staff I hava a data set provided by ADNI initiative, which is formed by a set of pre-processed T1-weighted MRI using FreeSurfer. The feature space consists of cortical thickness and subcortical volumes. Well, I want to vis

Re: [Freesurfer] Longitudinal Gray/white Contrast Measure

Hi William, you can use freesurfer's pctsurfcon to compute the gray/white contrast on the longitudinal directories. This will produce a surface overlay at: tp.long.base/surf/?h.w-g.pct.mgh I don't think the long_mris_slopes script can deal with those files directly, so you have two options: -

Re: [Freesurfer] Longitudinal processing

Hi Falk, yes, the output of long_mris_slopes and long_stats_slopes is in percent (100 * rate / value_of_fit_at_mid_time). Also running 1mm data is different (as you know :-) from .8 so maybe you would analyze both separately, e.g. creating one base on 1mm time points and another on the .8mm ?

[Freesurfer] mri_vol2surf for functional 4D BOLD data only mapping 1 frame

External Email - Use Caution Hi There, I’m currently trying to run mri_vol2surf on some animal data and surfaces I’ve been working with. I’m having a bit of a problem with the command mri_vol2surf. I seem to be able to project my functional volume to my surface, however I’m curr

[Freesurfer] mni152reg ends with (ERROR: flirt)

External Email - Use Caution Dear Freesurfer Experts! The idea is to transform freesurfer output in to the MNI 1mm space using following command: mni152reg --s subject_id --1 But mni152reg crashes with following error: flirt.newdefault.20080811.sch terminate called after throwi

Re: [Freesurfer] Longitudinal processing

External Email - Use Caution Hi Martin, thanks for your quick reply and the clarification regarding the output. I have processed the 1 and 0.8 mm separately, so one base for each subject and resolution - no mixing has been conducted! :) Actually, I want to look into changes due

[Freesurfer] tractstats2table error

External Email - Use Caution Hello, I just ran trac-all on my data and am trying to use tractstats2table to run some tract-based group level analysis. I have created a text file with the full paths to each conditions stats file (attached below and tried to run the following comma

Re: [Freesurfer] tractstats2table error

External Email - Use Caution Sorry, I realized I used the pathstats.byvoxel.txt instead of pathstats.overall.txt. Attached is the correct .txt file and the new error I get from the python script called by tractstats2table pathstats.overall.txt Parsing the .stats files Building

Re: [Freesurfer] How can I visualize cortical thickness data on a brain template?

Hi Alberto yes, you should be able to. Do you have the individual datasets or some type of average? cheers Bruce On Mon, 13 May 2019, albertotricker wrote: >External Email - Use Caution > > Hello FreeSurfer technical staff > > I hava a data set provided by ADNI initiative, which is fo

Re: [Freesurfer] spatial scale bar question

Yes Bruce. It doesn't work. I appreciate if you could let me know when you had any updates on it. Thanks Mona From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Friday, May 10, 2019 6:15:05 PM To: Freesurfer support list Subject:

Re: [Freesurfer] spatial scale bar question

Hi Mona sure. As I said it is a bit more complicated than it seems. Ruopeng will post a note when something usable is in the dev version Bruce On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote: Yes Bruce. It doesn't work. I appreciate if you could let me know when you had any updates on

Re: [Freesurfer] spatial scale bar question

Great! Thanks > On May 13, 2019, at 9:56 AM, Bruce Fischl wrote: > > Hi Mona > > sure. As I said it is a bit more complicated than it seems. Ruopeng will post > a note when something usable is in the dev version > > Bruce > > > On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote: > >> Yes Bruc

[Freesurfer] Spatial smoothing kernel in fsfast

External Email - Use Caution Dear Freesurfer experts. Now I am using preproc-sess to preprocess functional MRI data. I would like to smooth the data first and then resample them into the standard space. Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run' first

[Freesurfer] MP2RAGE recon using Siemens Terra 7T scanner

External Email - Use Caution Hi Freesurfer users, we have a new Terra 7T scanner and I'm having issues collecting a clean MP2RAGE scan and subsequently reconstructing it. Does anyone with experience with this scanner have any suggestions about modifications to the standard Siem

Re: [Freesurfer] MP2RAGE recon using Siemens Terra 7T scanner

I would use the high res stream I made for the HCP ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ On 5/13/19 4:23 PM, Fuller-Deets, Josh (NIH/NEI) [C] wrote: > > External Email - Use Caution > > Hi Freesurfer users, > > > we have a new Terra 7T scanner and I'm havin

[Freesurfer] Research Assistant Position at Massachusetts Eye and Ear/Harvard Medical School in Boston, MA

The Laboratory for Visual Neuroplasticity at the Massachusetts Eye and Ear Infirmary (Harvard Medical School), located in Boston, MA is seeking a full-time research assistant to start between July and September 2019. Candidates who would be able to commit to the position for a minimum of two ye

[Freesurfer] check FS to native registration in freeview

External Email - Use Caution Hi, After bbregister, I ran mri_label2vol to convert a segmentation file to native functional space mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o aseg-in-func.nii --temp example_func.nii Now I would like to check how well the e

[Freesurfer] Geometric distortion

External Email - Use Caution Hi experts, I have following question from one of the reviewers regarding recon-all pipeline: *"Was geometric distortion corrected? If not, this should be discussed or mentioned in the study limitation."* I was wondering if the reviewer is referring to

Re: [Freesurfer] Geometric distortion

External Email - Use Caution There are different kinds of geometric distortion that affect your data to differing extents. What kind of MRI data was in your study? Matt. From: on behalf of Martin Juneja Reply-To: Freesurfer support list Date: Monday, May 13, 2019 at 6:53 PM

Re: [Freesurfer] check FS to native registration in freeview

you have to use the output of mri_label2vol in the freeview command On 5/13/2019 5:02 PM, Sam W. wrote: External Email - Use Caution Hi, After bbregister, I ran mri_label2vol to convert a segmentation file to native functional space mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat -

Re: [Freesurfer] Geometric distortion

External Email - Use Caution Thank you Matthew for your reply. I just ran recon-all to get cortical thickness, area and volume values for specific ROIs using the steps here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and correlated the morphometric values