Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Yes the output appears ok. I was under the impression there would be benefits from using the -hires flag with submillimeter T1s as input. If you suggest not having to use the -hires flag in our case (because of little benefit from 0.8mm input

Re: [Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

External Email - Use Caution > Hi, group analysis. I would like to perform a simple correlation analysis within group, aiming to map the clusters reporting the correlation between the FC and the seed volume or neuropsychological test scores (e.g. MMSE). Overall, the

Re: [Freesurfer] Freesurfer and crypt

Hi Bennet, I’m attaching a compressed tar file, chklc_fips.tgz, that is an attempt at creating a binary (chklc_fips) that uses its own local version of crypt. See the README file when you untar the archive. This is not officially supported in any way, and while it can read my license file

Re: [Freesurfer] mni152reg yields bad registration

External Email - Use Caution Thanks Doug, Yeah, I’m confused as to what happened with that registration too. I just used ANTs to do the warping and that worked well. Good to know about mri_cvs_register though, I will try to use that next time. -jared On 4/19/18, 12:12 PM,

[Freesurfer] Brainhack Donostia 2018

External Email - Use Caution Hello Everyone The Basque Center on Cognition Brain and Language (BCBL) will host the first edition of the BrainhackDonostia2018. The event aims at bringing together students and scientists at all levels of their careers to enjoy science and a

Re: [Freesurfer] QDEC Interaction of Two Covariates

QDEC is mostly depreicated. Use the command-line stream. See the group analysis on this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial On 04/19/2018 04:48 PM, David S Lee wrote: > > > Hi FreeSurfer Experts, > > I want to test the relationship between cortical thickness and two >

Re: [Freesurfer] Calculation of surface area

We output surface area separately both as a map and as statistics On 04/19/2018 04:47 PM, Zohar Berman wrote: > Dear FreeSurfer experts, > > Can one use the volume and cortical thickness of a region to calculate > the surface area of this region? > > Thanks a lot in advance! > Best, > Zoi > > >

[Freesurfer] Calculation of surface area

External Email - Use Caution Dear FreeSurfer experts, Can one use the volume and cortical thickness of a region to calculate the surface area of this region? Thanks a lot in advance! Best, Zoi ___ Freesurfer mailing list

[Freesurfer] QDEC Interaction of Two Covariates

External Email - Use Caution Hi FreeSurfer Experts, I want to test the relationship between cortical thickness and two continuous covariates (interaction) while controlling for one categorical variable. In QDEC, I can only choose one covariate, so I created a new variable that is

Re: [Freesurfer] Recon-all with custom atlas

External Email - Use Caution Thanks for your patience with me. I am really appreciate. : ) Ting > On Apr 19, 2018, at 3:14 PM, Douglas N. Greve wrote: > > The wiki and the papers :) > > > On 04/19/2018 03:22 PM, Ting Li wrote: >> External Email

Re: [Freesurfer] Recon-all with custom atlas

The wiki and the papers :) On 04/19/2018 03:22 PM, Ting Li wrote: > External Email - Use Caution > > Douglas, > > Thanks for your quick response. If I only want the information of cortical > thickness, surface area, volume for various cortical regions and LGI, then > the Freesurfer

Re: [Freesurfer] Recon-all with custom atlas

That is, but since that wiki was written, I've written a script called make_folding_atlas. It takes quite a while to run through the 10 or so iterations. You might not need it as surface-based registration is much less sensitive to brain changes than volume-based. On 04/19/2018 04:05 PM, Ting

Re: [Freesurfer] Recon-all with custom atlas

External Email - Use Caution Douglas, I have one more question. Do I need an accurate surface template for my surface-based analysis? Does this ( https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates

Re: [Freesurfer] Recon-all with custom atlas

External Email - Use Caution Douglas, Thanks for your quick response. If I only want the information of cortical thickness, surface area, volume for various cortical regions and LGI, then the Freesurfer template is good enough and I don’t need to apply my own template. This is

Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Hi Jim, >From my experience .8 isotropic is on the edge. Did you take a look at the >output? You can always send us the data if you want us to take a look. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging

Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Thanks. I ran several subjects that were native 0.82 x 0.82 x 0.85mm through the standard recon-all -all stream, with the -hires flag (but with no experts file). The volumes and surafces look good. Is there any need to be concerened with the output

Re: [Freesurfer] recon all error mpr2mni305

Hi Richard, it seems this was caused by a minor update to our mac build machine. These libraries should be correctly linked now in the most recent dev build (updated a few minutes ago). Let me know if you still have issues best, Andrew On 4/19/18, 2:39 PM,

Re: [Freesurfer] recon all error mpr2mni305

External Email - Use Caution Message: 1 Date: Thu, 19 Apr 2018 12:05:03 -0400 From: "Douglas N. Greve" Subject: Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305 To: Message-ID:

Re: [Freesurfer] LGI for the lobar annotation

External Email - Use Caution Thank you!! :D On Thu, Apr 19, 2018 at 12:57 PM Douglas N. Greve wrote: > yes > > > On 04/19/2018 07:17 AM, Fernanda Hansen P. de Moraes wrote: > > Douglas, thank you very much again. > > So I can assume it is the lGI for the

Re: [Freesurfer] Recon-all with custom atlas

No, I think that is it. On 04/19/2018 02:07 PM, Khoi Mai wrote: > > External Email - Use Caution > > From what I read in the gctrain --help, does it only require > talairach_man.xfm and the manual segmentation files? Does it require > anything else for each subject? > > On Thu, Apr 19,

Re: [Freesurfer] Recon-all with custom atlas

External Email - Use Caution From what I read in the gctrain --help, does it only require talairach_man.xfm and the manual segmentation files? Does it require anything else for each subject? On Thu, Apr 19, 2018 at 12:39 PM, Douglas N. Greve wrote: > If

Re: [Freesurfer] Recon-all with custom atlas

If you want to do a surface-based analysis, then you don't need to have an accurate volume template. If you want to use a custom volume-based segmentation atlas, then you'll need to run gcatrain and gca-apply On 04/19/2018 01:28 PM, Ting Li wrote: > External Email - Use Caution > >

Re: [Freesurfer] Recon-all with custom atlas

I'm not clear on what you are trying to do. Did you apply the atlas to an individual and have the atlas ROIs in the individual brain? On 04/19/2018 12:42 PM, Ting Li wrote: > > Douglas, > > Thank you so much for your response. My atlas is nii.gz format. What should I > do to get the

Re: [Freesurfer] Recon-all with custom atlas

External Email - Use Caution Douglas, Sorry for bother you again. Our group want to study a cohort children’s brain using Freesurfer. We prefer to register our subjects to a custom children template. The template basically is an average of all the subjects we are going to

Re: [Freesurfer] unable to open freeview

External Email - Use Caution Hi Andrew, I did close it and reopen it. There seem to be two different errors in this output. If I just run echo $PATH, I get:

Re: [Freesurfer] unable to open freeview

Did you close and open a new terminal window first? Sorry, I forgot to mention that the bash_profile needs to be re-sourced if you make changes. After this, run “echo $PATH” to make sure that the brew error is no longer present Andrew From: Darko Komnenić Date: Thursday,

Re: [Freesurfer] unable to open freeview

External Email - Use Caution Hi Andrew, I commented out the last two lines, and the same error message still appears. Please let me know if you have any other suggestions. Thanks! Best, Darko On Thu, Apr 19, 2018 at 6:08 PM, Hoopes, Andrew wrote: > Hi

Re: [Freesurfer] Recon-all with custom atlas

External Email - Use Caution Douglas, Thank you so much for your response. My atlas is nii.gz format. What should I do to get the cortical thickness, surface area and volume for various cortical regions? Thanks in advance. Best, Ting > On Apr 19, 2018, at 11:28 AM, Douglas

Re: [Freesurfer] Recon-all with custom atlas

Is the atlas in GCA format? If so, then you can use gca-apply On 04/19/2018 10:09 AM, Ting Li wrote: > Hi Freesurfer Experts, > > We want to run recon-all with a custom atlas which is generated from > ANTs multivariate template construction. What is the right procedure > to run recon-all? Run

Re: [Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

I'm not sure what you mean. Can you elaborate? Is this an individual analysis or a group analysis? On 04/18/2018 10:10 AM, std...@virgilio.it wrote: > > Hi list, > > which the best way to perform a whole-brain correlation of the FC > assessed by FS-FAST with the volumetic or neuropsychological

Re: [Freesurfer] mni152reg yields bad registration

I don't know what might have happened (under the hood, mni152reg uses the FSL flirt program). If you want a non-linear registration, then you'll need to use CVS (mri_cvs_register) and choose the mni target. If you just want the aparc of the aparc+aseg, then don't go into the volume at all.

Re: [Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness

The group analysis for more complicated designs is the same as for thickness analysis and can be found, eg, here https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples It will only analyze the dat you give it (ie, bold amplitude, cvr, thickness) On 04/17/2018 02:23 PM, Arsenije Subotic wrote:

Re: [Freesurfer] unable to open freeview

Hi Darko, try commenting out the last two lines and rerunning freeview (it’s possible that the error message getting inserted into your PATH is the source of these issues): # export PATH="$HOME/.linuxbrew/bin:$PATH" # export PATH="$(brew --prefix)/bin:$PATH" From: Darko Komnenić

Re: [Freesurfer] How FDR was used to correct for multiple comparisons

Yes, that looks right. It is the basic FDR computation On 04/18/2018 12:53 PM, Livia Liu wrote: > > Dear Douglas, > > Thank you for your reply. I read the related FDR paper given in the > “mri_fdr –help”. > > Please tell me if the FDR correction in FreeSurfer do like the below. > > For the V

Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

How does the input image look, ie, orig.mgz? On 04/19/2018 09:49 AM, Jones, Richard wrote: > > I ran the command shown below to do recon-all on DICOM images from a > Philips Ingenia scanner using the development version of freesurfer on > a Mac running high Sierra. > > recon-all -i >

Re: [Freesurfer] LGI for the lobar annotation

yes On 04/19/2018 07:17 AM, Fernanda Hansen P. de Moraes wrote: > Douglas, thank you very much again. > So I can assume it is the lGI for the area (in this case the lobe)? > > Thank you again! > > On Wed, Apr 18, 2018 at 11:48 PM Douglas Greve

[Freesurfer] SLURM - speed processing

External Email - Use Caution Hi all, I'm definitively a noob with both freesurfer and SLURM processes and I wonder if anyone could give me some advice. I tried processing a subject (including hippocampal segmentation) using the following command (freesurfer 6.0.0): recon-all

Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

Hi Richard, thanks for pointing this out – I’ll take a look into it. best Andrew From: on behalf of "Jones, Richard" Reply-To: FS Help Date: Thursday, April 19, 2018 at 9:49 AM To: FS Help

Re: [Freesurfer] Freesurfer and crypt

External Email - Use Caution Hi, Rob, The call to crypt() appears to be in FreeSurfer's license validation routine, since it is immediately after reading the license file. In the sense that FreeSurfer cannot run without some sort of license, and that license validation is using

[Freesurfer] Recon-all with custom atlas

External Email - Use Caution Hi Freesurfer Experts, We want to run recon-all with a custom atlas which is generated from ANTs multivariate template construction. What is the right procedure to run recon-all? Run recon-all to my atlas itself first and them use this output as a

[Freesurfer] hippocampal segmentation development version question

Hi, I am interested in using the head/body/tail output from the hippocampal subfield segmentation module. Is there a reference or description of what landmarks were used to separate head/body and body/tail? Thanks! Maureen ___ Freesurfer mailing list

[Freesurfer] Freesurfer dev version : recon all error mpr2mni305

I ran the command shown below to do recon-all on DICOM images from a Philips Ingenia scanner using the development version of freesurfer on a Mac running high Sierra. recon-all -i /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm -subject HOPE_SS020 -all The program crashed with the

Re: [Freesurfer] LGI for the lobar annotation

Douglas, thank you very much again. So I can assume it is the lGI for the area (in this case the lobe)? Thank you again! On Wed, Apr 18, 2018 at 11:48 PM Douglas Greve wrote: > The "intensity" is the mean value of the input (lh.pial_lgi in this case) > averaged over

Re: [Freesurfer] unable to open freeview

An update, in the .bash_profile file, there is a line about linuxbrew. Do you recommend that I remove it? Sending the file attached. Best, Darko On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić wrote: > Hi Andrew, > sorry for the delay. Attached is the hidden bashrc file

Re: [Freesurfer] unable to open freeview

Hi Andrew, sorry for the delay. Attached is the hidden bashrc file from my Home folder. It doesn't seem to specify anything about linuxbrew, so I don't know why this error is showing up. Thanks a lot for any suggestions! Best, Darko On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew