Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

According to Bruce's request I repost the rest of thread: We set up our our hippocampal subfield T2 protocol based on the ADNI protocol (with some minor differences) as suggested by Iglesias. However, we see an artefact similar to the image found in ADNI2 training manual (page 28): http://adni.lon

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)

Hi Martin, thank you so much for your detailed answer. I will see how we can implement these modifications. Just two quick follow up questions: 1) I have half of the data already processed with the CROSS step using FS 5.3.0. Is it possible to use this data when running the TEMPLATE and LONG s

Re: [Freesurfer] Invalid MEX file - FS dev-version error?

Dear Reetta Check if you’ve got the right compiler for the MEX files. Regards, Fereshte On Tue, Feb 27, 2018 at 2:10 PM Reetta-Liina Armio wrote: > Dear Freesurfer developers, > > I have run basic segmentation (and hippocampal segmentation) with > Freesurfer 6.0. I have now tried to run amygdala

Re: [Freesurfer] Invalid MEX file - FS dev-version error?

Thank you, but what exactly should I do? -Reetta-Liina Armio Lähetetty iPhonesta > Fereshte kirjoitti 27.2.2018 kello 13.00: > > Dear Reetta > Check if you’ve got the right compiler for the MEX files. > Regards, > Fereshte >> On Tue, Feb 27, 2018 at 2:10 PM Reetta-Liina Armio wrote: >> Dear F

Re: [Freesurfer] Hippocampal Subfield Error

Dear Theo, Would you mind sending up the log of the hippocampal subfields as well? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of "AKUDJEDU, THE

[Freesurfer] Novice have a problem

Hi all, very nice to find a place to ask all the fs giants a question. I run recon-all …-all -localGI, which always return this at the end. Can anyone help me find out what I need to do to evade this error? Every time I delete the shortcut folder created during the process and copy the fsaverage

Re: [Freesurfer] Novice have a problem

Also, are there ways to manually generate *h.pial-outer-smoothed and other related files, so as to accomplish the final step for iElvis if the *h.pial-outer-smoothed files and a bunch of *h.pial* files are missing? Best！ 在 2018年2月27日，06:52，shilin18 mailto:shili...@stanford.edu>> 写道： Hi all,

Re: [Freesurfer] Quality issues when running recon-all

Hi Adrian it's impossible for us to diagnose without more information. What was the acquisition (field strength, resolution, sequence type, etc...) and at least send us the contents of the recon-all.log file. cheers Bruce On Tue, 27 Feb 2018, adriancarl.stei...@uzh.ch wrote: Dear Freesurf

Re: [Freesurfer] Hippocampal Subfield Error

Hi Theo, Sorry for not being more clear; I meant hippocampal-subfields-T1.log, which should be in the directory “scripts”. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.a

Re: [Freesurfer] Creating ROI on the functional map

I apologize. I was wrong. Thanks, S On Mon, Feb 26, 2018 at 5:16 PM, Sarah Cole wrote: > It doesn't work on tksurfer. But it's ok. > > So Doug, is this the latest tutorial: https://surfer.nmr.mgh. > harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview for > FS-FAST and creating funct

[Freesurfer] Freeview update on Mac

Hi Doug/Zeke, Could you please update the page for freeview update on Mac- if it is available. https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.

Re: [Freesurfer] Invalid MEX file - FS dev-version error?

I’m not sure about MATLAB 2014b but you need to have installed Microsoft Visual c++ ( 2008 works fine with R2014a) and Fortran to compile MEX files; that may be the problem. Cheers On Tue, Feb 27, 2018 at 3:42 PM Reetta-Liina Armio wrote: > Thank you, but what exactly should I do? > > -Reetta-L

Re: [Freesurfer] Antwort: Re: Quality issues when running recon-all

no worries. That is a pretty short TR and a pretty long TE for a typical T1-weighted scan. Do you know what kind of scan it was? That is, the name of the sequence (e.g. FLASH, MPRAGE, SPGR, etc...) cheers Bruce On Tue, 27 Feb 2018, adriancarl.stei...@uzh.ch wrote: Hi Bruce Thank you very mu

Re: [Freesurfer] Freesurfer Digest, Vol 168, Issue 54

at 15:31 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Hippocampal Subfield Error Dear Eugenio, Attached as requested. Thanks Theo -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/piperm

[Freesurfer] demean age in CT analysis in QDEC?

Dear Freesurfer developers, I'm running a standard cortical thickness analysis between 2 patient groups (patients with schizophrenia with hallucinations (H) vs. patients with schizophrenia without hallucinations (NH)). I'm looking at the main effect of group (H vs. NH), while controlling for s

[Freesurfer] mir_vol2surface registration file error

Hello, We are trying to project a volume map onto a surface. Our network based volume map is a .vmp file and our surface is a nifti file. We were able to convert the volume maps from .vmp to nifti. Our volume map is: negative_allsocial_proportion.nii Our surface is: SN_like_cortical_lh.nii The out

Re: [Freesurfer] Freeview update on Mac

Hi Sarah, I updated the wiki page. We actually just put up a standalone, dev freeview app today. best Andrew On February 27, 2018 at 11:38:57 AM, Sarah Cole (coleashle...@gmail.com) wrote: Hi Doug/Zeke, Could you please update the page for freeview update on M

[Freesurfer] missing '*h.pial*' files, cannot find fseverage folder.

Hi all, very nice to find a place to ask all the fs giants a question. I run recon-all …-all -localGI, which always return this at the end. Can anyone help me find out what I need to do to evade this error? Every time I delete the shortcut folder created during the process and copy the fsaverage

Re: [Freesurfer] Invalid MEX file - FS dev-version error?

Hi! The problem changed a bit since I downloaded the Matlab runtime compiler 2014b as the Freesurfer suggested. See the problem below. Here are the details: Bugr: - FREESURFER_HOME: /Applications/freesurfer_5_270218 Bu

Re: [Freesurfer] Invalid MEX file - FS dev-version error?

You’re missing your license file. https://surfer.nmr.mgh.harvard.edu/fswiki/License -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Reetta-Liina Armio Reply-To:

[Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

Hello FreeSurfer experts, I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035" Whenever I try, I receive the following error (in error.log file); CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15

[Freesurfer] Images fail to convert

Dear Experts, I am trying to process a some T1 data through FreeSurfer 5.3.0, but it seems to fail during the first format conversion step. This data is from a multicenter study so I am not familiar with the acquisition details although the images visually look ok. Any suggestions? Thanks, C

Re: [Freesurfer] thickness measure in basal ganglia

Yes, I mean a cerebellar parcellation. Do you project to distribute them. Thanks Giovanni Envoyé de mon iPhone > Le 26 févr. 2018 à 15:17, Bruce Fischl a écrit : > > Hi Giovanni > > do you mean a cerebellar parcellation? We have several prototypes but haven't > distributed anything yet. >

[Freesurfer] Freesurfer Input Imaging

Hello, is there any recommendation from Freesurfer for MRI images used during recon-all? i.e., should we use a sagittal MRI, coronal or transversal? For instance, I have one subject with these 3 different orientations. I ran recon-all on the 3 of them and got the results for the reconstruction

Re: [Freesurfer] Freesurfer Input Imaging

Hi Daniel these days you are better off getting a single 3D acquisition like MPRAGE rather than 3 orthogonal (thick slice) ones. cheers Bruce On Tue, 27 Feb 2018, Daniel Alejandro Reyna Torres wrote: Hello, is there any recommendation from Freesurfer for MRI images used during recon-al