[Freesurfer] How to get the difference between motion, NU

2019-05-13 Thread chen
External Email - Use Caution Hi expert, I selected hippocampus and amygdala as ROIs to estimated the reliability of a well-controlled multi-site study. The travelling volunteers were scanned in each site with the same type scanners and scan protocol. But, amygdala volume

Re: [Freesurfer] Longitudinal Gray/white Contrast Measure

2019-05-13 Thread Martin Reuter
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: -

[Freesurfer] mni152reg ends with (ERROR: flirt)

2019-05-13 Thread vin rasa
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

Re: [Freesurfer] tractstats2table error

2019-05-13 Thread Daniel Callow
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

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

2019-05-13 Thread Robert Austin Bruce Benn
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

Re: [Freesurfer] Longitudinal processing

2019-05-13 Thread Martin Reuter
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] How can I visualize cortical thickness data on a brain template?

2019-05-13 Thread albertotricker
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

[Freesurfer] tractstats2table error

2019-05-13 Thread Daniel Callow
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

Re: [Freesurfer] Longitudinal processing

2019-05-13 Thread falk.luesebr...@med.ovgu.de
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

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

2019-05-13 Thread Bruce Fischl
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

Re: [Freesurfer] spatial scale bar question

2019-05-13 Thread Nasiriavanaki, Zahra
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:

[Freesurfer] MP2RAGE recon using Siemens Terra 7T scanner

2019-05-13 Thread Fuller-Deets, Josh (NIH/NEI) [C]
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

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

2019-05-13 Thread Greve, Douglas N.,Ph.D.
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

[Freesurfer] check FS to native registration in freeview

2019-05-13 Thread Sam W.
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

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

2019-05-13 Thread Bailin, Emma
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

Re: [Freesurfer] spatial scale bar question

2019-05-13 Thread Nasiriavanaki, Zahra
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

Re: [Freesurfer] spatial scale bar question

2019-05-13 Thread Bruce Fischl
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

[Freesurfer] Spatial smoothing kernel in fsfast

2019-05-13 Thread Zhi Li
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'

[Freesurfer] Geometric distortion

2019-05-13 Thread Martin Juneja
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

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

2019-05-13 Thread Greve, Douglas N.,Ph.D.
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

2019-05-13 Thread Glasser, Matthew
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

Re: [Freesurfer] Geometric distortion

2019-05-13 Thread Martin Juneja
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