Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

mais_ca_label
by Valentina Mancini 19 Jul '19

19 Jul '19

External Email - Use Caution Dear Freesurfer experts, we are trying to use your function "mris_ca_label" in order to get an annotation file in the subject's space using the Schaefer-Yeo atlas. However, we noticed that a "special classifier array" is required among the inputs. Could you pleas give us more information about the type of file required and where we can find it? Thank you and best regards, Valentina Mancini

3 3

QDEC interpretation question - Please respond
by Avi Gharehgazlou 19 Jul '19

19 Jul '19

External Email - Use Caution Hi, I have a question regarding interpreting results from QDEC. I am investigating lGI in individuals with ASD and controls (which I will refer to as 'TD' here). I understand from the archives that when "TD" is listed first and "ASD" is listed second in my "diagnosis.levels" file, when I select the question "Does average lGI, accounting for sex, differ between TD and ASD?" results would be interpreted as: Yellow regions = greater lGI in TD; blue regions = reduced lGI in TD. Assuming the same order, I thought that since I listed "females" first and "males" second on my "sex.levels" file, then results from selecting question "Does average lGI, accounting for diagnosis, differ between females and males?" would be interpreted as: Yellow regions= greater lGI in females; blue regions = reduced lGI in females. Is this correct? The reason I'm asking is that when I extract mean lGI values of significant clusters (between females and males in the latter case above) and plot the mean lGIs for males and females separately, I see that the yellow regions show greater lGI in males instead of females! Will you please clarify for me how I have to interpret these results Thanks so much Avi

1 0

Patient vs group of controls
by m s 18 Jul '19

18 Jul '19

External Email - Use Caution Hello Freesurfer experts! I need to compare one patient to a group of controls and I wanted to know which is the best way to do this. Is it correct to do it with group analysis when 1 group only has one patient, thus no stdev, and the other group (controls) has for ex 20 patients? Is there a better choice for this situation or a prefered way to visualize result in this case?? Thank you! Mercedes

2 2

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"
by Greve, Douglas N.,Ph.D. 18 Jul '19

18 Jul '19

In freeview, you can use :overlay_color=colorscale,settings maybe Ruopeng can weigh in on exactly what to set them to to get the colorwheel Are you also looking to have freeview snap pictures for you? On 7/18/19 11:57 AM, Matthieu VANHOUTTE wrote: > External Email - Use Caution > Sorry not to be precise on my answer. > > I can easily open freeview to load overlay on surface and configure > the color scale to "Color Wheel". > > However to create pictur es for article I automatize the creation > of those pictures by scripting using tksurfer command line. There are > different options for this command line but I didn't find any option > to set the color scale to which I want "Color Wheel". > > Is there any tool existing allowing to use "Color Wheel" color scale > by scripting ? > > Best, > > Matthieu > > On 18/07/2019 17:51, Greve, Douglas N.,Ph.D. wrote: >> I don't know what you mean by "stay graphical". can you explain? What is >> the tksurfer option to load the colorwheel? >> >> On 7/18/19 11:47 AM, Matthieu VANHOUTTE wrote: >>> External Email - Use Caution >>> Hi Douglas, Bruce, >>> >>> Freeview is really nice but stay graphical. When I want to create >>> composed snapshots of surface overlays I use tksurfer with command >>> lines to create these. >>> >>> I looked at tksurferfv with command lines but didn't see where is the >>> option to set color scale to "Color Wheel"? >>> >>> Best, >>> >>> Matthieu >>> >>> On 18/07/2019 17:22, Greve, Douglas N.,Ph.D. wrote: >>>> There is a program called tksurferfv that runs freeview but takes all >>>> the same command line args as tksurfer >>>> >>>> On 7/18/19 10:56 AM, Bruce Fischl wrote: >>>>> Hi Matthieu >>>>> >>>>> tksurfer has been deprecated for years. Is there a reason you can't >>>>> switch to freeview? >>>>> >>>>> cheers >>>>> Bruce >>>>> On Thu, 18 Jul 2019, Matthieu VANHOUTTE wrote: >>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> Dear experts, >>>>>> >>>>>> I use tksurfer in command line to generate multiple faces images of >>>>>> overlays on the fsaverage surface. >>>>>> >>>>>> Graphically it is possible via freeview to set the color scale of >>>>>> the >>>>>> overlay with "Color Wheel" setting. I searched into the tksufer >>>>>> command >>>>>> help but didn' t find any option to specify this color scale. Doas >>>>>> anyone know how to deal with it by command lines ? >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Matthieu >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail.

2 1

voxel coordinates of corpus collosum
by Sadia Sheikh 18 Jul '19

18 Jul '19

External Email - Use Caution Dear Freesurfer experts How can I get the voxel coordinates of the segmented corpus callosum? I tried using the command mri_vol2label and id of the corpus callosum as 192 as given in Freesurfer LUT, but it gives an error: found no voxels matching id 192 Thanks in advance Sadia

3 9

How to make a SlicDelayFile in FSFAST
by Zhi Li 18 Jul '19

18 Jul '19

External Email - Use Caution Dear Freesurfer experts, May I ask how to create a slice delay file for slice timing in fsfast? Is there an example? The slice order of my data is [33:-2:1 32:-2:2], how could I convert this vector to time fraction of TR? I have checked the help information of slicetimer of FSL, but it is unclear to me and I did not found an example of it. Any suggestions? Thanks and best regards, LIzhi

1 0

Command line tksurfer: use of the color scale "Color Wheel"
by Matthieu VANHOUTTE 18 Jul '19

18 Jul '19

External Email - Use Caution Dear experts, I use tksurfer in command line to generate multiple faces images of overlays on the fsaverage surface. Graphically it is possible via freeview to set the color scale of the overlay with "Color Wheel" setting. I searched into the tksufer command help but didn' t find any option to specify this color scale. Doas anyone know how to deal with it by command lines ? Best regards, Matthieu

3 2

FLAIR data to improve pial surfaces
by Leyton Moscoso, Cristian Eduardo 18 Jul '19

18 Jul '19

Dear Freesurfer experts, I want to improve pial reconstruction by using FLAIR images in the pial reconstruction (freesurfer v6.0). Ø recon-all -subject subjectname -FLAIR /path/to/FLAIR_volume -FLAIRpial -autorecon3 T1 was acquired in a 3T Phillips scanner with a isometric voxel size of 1 mm3, whereas FLAIR images have a voxel size of 0.5 x 0.5 x 3.5 mm. Is there any issue in using different voxel sizes? Thank you Dr Cristian Leyton M Research Fellow in Neurology Department of Neurology Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

2 1

(no subject)
by 许飞飞 18 Jul '19

18 Jul '19

External Email - Use Caution Dear Freesurfer experts, I want to know how Freesufer to compute the volume and area at each vertex. Are there any references? I just found the reference which introduces the measure of thickness(MacDonald et al.2000). Any help with this would be greatly appreciated. Best regards, Feifei

2 2

DF for Longitudinal LME
by Bronwyn Overs 18 Jul '19

18 Jul '19

External Email - Use Caution Dear Freesurfer Mailing List, I am trying to calculate the effect size of the main and interaction effect clusters that were significant in my vertex-wise LME analysis. For this I need the degrees of freedom for each contrast, but I am confused about how to derive this. My input sample has 218 subjects (153 with 2 time-points, 65 with 1 time-point). The effects for which I need the degrees of freedom are: 1) Main effect of years in the control group (n=112) 2) Main effect of years in the case group (n=106) 3) Main effect of group at baseline (group has two levels, 0 or 1) 4) Interaction between years and group Any assistance you can provide would be great. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer