[Freesurfer] Before recon-all, is it necessary to set origin of the image?

Dear all, I'm new on FreeSurfer. I want to calculate cortical thickness, hippocampus volume from MRI images (obtained from ADNI). After installation, I tried recon-all. >> Only this process, can I obtain cortical thickness and hippocampus volume? And someone told me that I have to set origin

[Freesurfer] Tracula_average_average center

Hi Anastasia, One of Tracula's output is the "pathstats.overal.txt" and in this file we have a list of numbers. Kindly what is the difference between the metrics average and the metrics average center also which one do you recommend to do statistic? Thanks, Mohamad _

Re: [Freesurfer] permission denied

Hi I’ve previously encountered the same error. I’ve also tried to change permission but that didn’t really work out for me. I have fixed it by installing libjpeg62-dev: Maybe the following command could fix your problem too? sudo apt-get install libjpeg62-dev Hope this might work for you? Ch

[Freesurfer] longitudinal data processing

Dear FS-experts Is there any command that I can use for caching my preprocessed data in the recon-all longitudinal stream, since this is possible through adding the -qcache option in the cross-sectional pipeline. Or maybe this is already automatically done without adding any option to the comma

[Freesurfer] freeview fault: PETSC Error ...

I recently downloaded and installed freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz . I had been running this version previously but had to reload everything due to a disk crash. recon-all -all goes to completion with no errors. freeview starts up fine but fails on loading a volume file

Re: [Freesurfer] prefrontal cortex label

thank you. which labels are normally included as prefrontal cortex for freesurfer purposes? On Thu, Oct 23, 2014 at 5:04 PM, Douglas N Greve wrote: > > You can use mri_annotation2label to break up the annotation into > individual labels, then use mris_label2annot to recombine selected > labels i

Re: [Freesurfer] Before recon-all, is it necessary to set origin of the image?

Hi Ngoaka no, you don't need to set the origin of the image. Just point recon-all at a single slice from the correct dicom series (of a highres T1-weighted scan) with the -i -all -s and you should be good to go cheers Bruce On Tue, 4 Nov 2014, CHONNIKAN JONGKREANGKRAI wrote: Dear all,

[Freesurfer] Quality of surface-based alignment

Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse th

Re: [Freesurfer] Before recon-all, is it necessary to set origin of the image?

Dear Bruce, Thank you for quick answer. I can use .nii file instead of dicom, right? Best Regards, Ngoak > On 4 พ.ย. 2557, at 22:06, Bruce Fischl wrote: > > Hi Ngoaka > no, you don't need to set the origin of the image. Just point recon-all at a > single slice from the correct dicom series (

Re: [Freesurfer] Fwd: Underinclusion of Gray Matter

You could also add a lot more voxels to the wm.mgz (beyond what is wm) and depending on the source of the problem, that could fix it. On Mon, 3 Nov 2014, Bruce Fischl wrote: Hi Christina it's tough to tell from just a single image, but it looks to me like you are missing a bunch of white mat

Re: [Freesurfer] longitudinal data processing

Hi Robby, depends on what you are trying to achieve. The first stats model we implemented was the 2-stage model (with a linear fit inside each subject and then a cross sectional comparison of the atrophy rates, ie. slopes of the fit). For the first step the surface data (within-subject) is al

Re: [Freesurfer] Quality of surface-based alignment

What criteria would you use to determine one alignment was better than another? Peace, Matt. From: "Caspar M. Schwiedrzik" Reply-To: Freesurfer support list Date: Tuesday, November 4, 2014 at 7:17 AM To: "Freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Quality of surface-based alig

Re: [Freesurfer] Fsaverage for ROI analysis of children

Hi Doug, Just wondering if you saw my response to your questions. Haven't heard anything from anyone else yet about my questions. Thanks in advance. In case you didn't see my response it is below: I made the ROI on an individual subject basis, not from fsaverage. Not sure if the labels I ma

Re: [Freesurfer] Quality of surface-based alignment

Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: > Hi Freesurfers, > I

Re: [Freesurfer] Before recon-all, is it necessary to set origin of the image?

yes, that's fine On Tue, 4 Nov 2014, CHONNIKAN JONGKREANGKRAI wrote: Dear Bruce, Thank you for quick answer. I can use .nii file instead of dicom, right? Best Regards, Ngoak On 4 พ.ย. 2557, at 22:06, Bruce Fischl wrote: Hi Ngoaka no, you don't need to set the origin of the image. Just poi

Re: [Freesurfer] prefrontal cortex label

I don't know. Maybe someone else can weigh in. doug On 11/04/2014 07:38 AM, Anna Jonsson wrote: > thank you. which labels are normally included as prefrontal cortex for > freesurfer purposes? > > On Thu, Oct 23, 2014 at 5:04 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > >

Re: [Freesurfer] Quality of surface-based alignment

Hi Bruce and Matt, I should specify that I am working with non-human primate data, so unfortunately, looking at the parcellations would not work. I am aligning individuals to a a custom template that I made. I was wondering whether there is maybe an output file that has something numerical on how m

Re: [Freesurfer] Quality of surface-based alignment

You can look at how well the curvature and/or sulcal maps from your template overlay on the individual. doug On 11/04/2014 11:46 AM, Caspar M. Schwiedrzik wrote: > Hi Bruce and Matt, > I should specify that I am working with non-human primate data, so > unfortunately, looking at the parcellation

Re: [Freesurfer] Quality of surface-based alignment

oh, I see. I would paint the folding patterns on the sphere.reg and toggle back and forth between them to see if they look right. Alternatively you could draw some sulci onto one of your datasets (this is easy to do in tksurfer) and use mri_label2label to map it to others and see if they land i

Re: [Freesurfer] Fsaverage for ROI analysis of children

In that case, can you just use the mean thickness values as listed in subject/stats/?h.aparc.stats ? On 11/04/2014 10:33 AM, Smith, Michael wrote: > > Hi Doug, > > Just wondering if you saw my response to your questions. Haven’t heard > anything from anyone else yet about my questions. Thanks i

Re: [Freesurfer] Quality of surface-based alignment

Thanks! But there is nothing like a number I could pull from the registration process, e.g. the distances of the vertices in registration space? Caspar 2014-11-04 11:51 GMT-05:00 Bruce Fischl : > oh, I see. I would paint the folding patterns on the sphere.reg and > toggle back and forth between t

[Freesurfer] mri_label2label

Dear all, I would like to draw a ROI on a group average surface (template) and map it back to the surface of individual subjects. For this, I would like to create the template based on my subjects, rather than using fsaverage. As far as I understood, I should first create the template by using:

[Freesurfer] mri_watershed -brain_atlas undocumented?

- This is a repost. It seems it did not come trough yesterday. Apologies if this becomes a double post - Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be foun

Re: [Freesurfer] mri_label2label

use --trgsurfreg sphere.reg.myAvg On 11/04/2014 12:27 PM, Roberta Santoro wrote: > > Dear all, > > I would like to draw a ROI on a group average surface (template) and > map it back to the surface of individual subjects. For this, I would > like to create the template based on my subjects, rat

Re: [Freesurfer] mri_watershed -brain_atlas undocumented?

Hi Tom I'll cc Flo who wrote this code (a long time ago!). I think the -brain_atlas flag takes a gca atlas and uses it to avoid large-scale errors, while -atlas uses some built-in statistics about the shape and size of e.g. the cerebellum to avoid erasing it accidentally. Flo can correct me if

[Freesurfer] Create surface Labels of equal size

Dear Freesurfers, I would like to mark the brain surface (fsaverage) for an illustration of stimulation areas (TMS). I have calculated coordinates in Vertex RAS and Vertex Talairach. They are correctly located on the fsaverage surface in tksurfer. Is there a way to create labels of equal sizes a

Re: [Freesurfer] Create surface Labels of equal size

Hi Bastian you should be able to do this with a tcl script in tksurfer. Take a look at the ones we distribute for some examples cheers Bruce On Tue, 4 Nov 2014, Bastian Cheng wrote: > Dear Freesurfers, > > I would like to mark the brain surface (fsaverage) for an illustration > of stimulation

Re: [Freesurfer] Create surface Labels of equal size

Hi Bruce, thank you! I looked up all commands here: http://freesurfer.net/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference I guess what I should do is 1) mark vertex at coordinate 2) create label at marked vertex 3) maybe dilate the label. does this sound right? On 4 November

Re: [Freesurfer] Create surface Labels of equal size

yes, exactly On Tue, 4 Nov 2014, Bastian Cheng wrote: > Hi Bruce, thank you! > > I looked up all commands here: > http://freesurfer.net/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference > > I guess what I should do is > > 1) mark vertex at coordinate > 2) create label at marked ver

[Freesurfer] Tracula_critical issue

Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the informatio

Re: [Freesurfer] freeview fault: PETSC Error ...

you can try downloading our nightly 'dev' build of freeview, from here: https://surfer.nmr.mgh.harvard.edu/fswiki/Download or here's a quicker way (this is a one-line command... wget ): wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin and copy