Re: [Freesurfer] Hippocampal subfield registration question.

External Email - Use Caution Hi Jamie, It’s a message from mri_robust_register in the initialization of the atlas position. If the finaloutput looks reasonable (which it mostly likely will), don’t worry too much. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research

Re: [Freesurfer] mri_volcluster not recognize --mindistance

Try --mindist not --mindistance On 8/9/18 9:08 AM, Yagmur Ozdemir 19 wrote: External Email - Use Caution Hello FreeSurfer experts, I am trying to run mri_volcluster with the following command to later create masks of clustered regions from functional data. I get an error saying

Re: [Freesurfer] Midline errors

HI Maxime check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote: External Email - Use Caution Hello FreeSurfer Developers,   I use

Re: [Freesurfer] Correlations on QDEC

did you see the text where it says "If you seek help with this problem, make sure to send:" and then it gives a list of things to send? There will be a file called y.fsgd in the output, make sure to send that On 8/8/18 4:40 PM, Avi Gharehgazlou wrote: External Email - Use Caution Hi

Re: [Freesurfer] T1 mapping

mri_fit_parms should do it. BTW, if you are using a siemens scanner, you should just collect an MP2RAGE. That automatically outputs a quantitative T1 map using the two inversion technique. The results are much more accurate than using multiple flip angles On 8/8/18 5:00 PM, Fotiadis,

Re: [Freesurfer] Surface Area in Toddlers/Children

Yes. -qcache actually calls mris_preproc. At one point, FS did not preserve total area when  mapping to fsaverage. I fixed it a while ago, but maybe something was still off in 5.1 On 8/10/18 2:06 PM, Derek Sayre Andrews wrote: External Email - Use Caution Hi Douglas, Thank you for

[Freesurfer] recon-all with mri_ca_normalize (longitudinal)

External Email - Use Caution Hello FreeSurfer team, In order to create the longitudinal base after norm.mgz, Is the command below the right way to end recon-all after creating norm.mgz? recon-all -s subjectID -autorecon1 -autorecon2 -i T1image -canorm. Thank you. Best, Paul

Re: [Freesurfer] Plotting QDEC results

Each row is a subject and each column is a cluster. BTW, a threshold of 1.3 is way too low for lGI. If you want to use a threshold that low, you should use permutation instead of monte carlo (in general, permutation is better, but certainly for lGI). On 8/9/18 1:39 PM, Avi Gharehgazlou wrote:

[Freesurfer] Hippocampal subfield registration question.

External Email - Use Caution Dear FS List, I was just started to run hippocampal subfield segmentation and had a question about registration (and a related output warning). In the ~5 test subjects I've tried the SF routine, I get a warning early on that says--

Re: [Freesurfer] Confusion about MRI_GLMFIT

On 8/8/18 2:17 PM, Funk, Quentin wrote: External Email - Use Caution Freesurfer experts, I'm trying to figure out what values I get from mri_glmfit as in the tutorial. In particular, I'm interested in how I can

[Freesurfer] New segmentation of thalamic nuclei

External Email - Use Caution Dear FreeSurfer users, It is my pleasure to announce that our new tool to segment the thalamic nuclei from structural MR scans is available in the development version of FreeSurfer. The tool relies on an atlas derived from manual annotations made on

Re: [Freesurfer] Surface Area in Toddlers/Children

It should be preserving total surface area. Can you send your mris_preproc command line and the terminal output? It might be something with 5.1 as well. On 8/9/18 3:49 PM, Derek Sayre Andrews wrote: External Email - Use Caution Dear Freesurfer Developers and Experts, I have been

Re: [Freesurfer] Viewing the output of mris_preproc in Freeview + export to Matlab

It is showing you the map of the first frame (subject in this case). You can adjust the frame with a slider on the left. Also, there is a time plot icon on the top. If you click on that it will show you a graph of the subjects at the chosen vertex. On 8/10/18 8:16 AM, Alon Baram wrote:  

Re: [Freesurfer] coregistering with bbregister

Sometimes the FSL initialization will fail. If you are using FS version 6, then run it without specifying --init-fsl and it will use mri_coreg, which is more robust. If your anatomical and functional were acquired at the same time, you might be able to get away with --init-header instead. On

Re: [Freesurfer] Surface Area in Toddlers/Children

External Email - Use Caution Hi Douglas, Thank you for the response. I did not use mris_preproc to prepared the data. The data was mapped to fsaverage using recon-all with -qcache. I then loaded the l/rh.area.pial.fwhm15.fsaverage.mgh files into MATLAB using

Re: [Freesurfer] Untar and sh files in dev version

Hello Schumman, Try the following command on the tar archive (cut and paste it if you like) $ tar zxpf freesurfer-linux-centos6_x86_64-dev.tar.gz and then take a look at the files. - Rob On Aug 10, 2018, at 10:25 PM, Schumman Resonance mailto:schumm...@gmail.com>> wrote: External

[Freesurfer] Untar and sh files in dev version

External Email - Use Caution Hi, Couple of newbie questions. I downloaded the dev version of freesurfer and did: tar xvzf freesurfer-linux-centos6_x86_64-dev.tar.gz to get gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive

Re: [Freesurfer] T1 mapping

Hi Doug, Thanks for your response! I had a couple follow-up questions: 1) If I used mri_fit_parms to calculate the T1 maps, then created a surface mid-cortex (with mris_expand) with that T1 map as a reference, and uploaded that file into MATLAB through MRIread, would the resulting values

Re: [Freesurfer] coregistering with bbregister

External Email - Use Caution Hi Doug, Thank you for your suggestions, I'll try them. Could you please let me know if my code is actually doing what I intend it to do? Specifically, the idea is to perform functional-to-structural registration. so first I did $ bbregister --t2

Re: [Freesurfer] Surface Area in Toddlers/Children

External Email - Use Caution Hi Derek, you could try creating a study-specific template to replace fsaverage with make_average_subject and then re-run your reconall. Best, Laurel Laurel Raffington Postdoctoral Researcher Center for Lifespan Psychology Max Planck

[Freesurfer] Viewing the output of mris_preproc in Freeview + export to Matlab

External Email - Use Caution Hello, I want to overlay the .mgh file which is the output of mris_preproc in freeview on the fsaverage surface. This file has (according to mri_info) the dimensions Nverteces x 1 x 1 x Nsubjects: my data in fsaverage space for each of my subjects.