[Freesurfer] LGI - output issue

External Email - Use Caution Good afternoon FreeSurfer experts, Hope that everyone is well and staying safe! I tried opening LGI freeview (or tksurferfv) output, and I have been running into the following issues (see code and error message outputs below). Any ideas how I could fi

[Freesurfer] FSFAST (mkcontrast-sess) with Octave

External Email - Use Caution Dear Surfers, I am trying to run fsfast mkcontrast-sess with octave. I used the following command: "mkcontrast-sess -analysis ../mkanalysis/ftap.sm05.lh -contrast ftap -a 1 -octave" I get the output below. I wonder if you could help me out? Am I m

[Freesurfer] LGI - trouble creating output file for each subject

External Email - Use Caution Hello again FreeSurfer experts, I am having some issues creating the output file with the LGI data for each subject. Could you please help me with this? See below the code (in bold) that I used and the outputs that I got. Please let me know if you need

Re: [Freesurfer] qcache option for post recon-all longitudinal data

On 8/6/2021 6:35 PM, Zeng, Qi wrote: External Email - Use Caution Hi Freesurfer experts, I've done running a longitudinal analysis pipeline for individuals in 3 groups. Now, I need to get prepared for QDEC group analysis. I cp all groups of individuals to the same directory and eac

Re: [Freesurfer] Fwd: Base correction, longitudinal analysis

That is just part of the way the long stream works. When you run a base subject, you have to spec all the cross tps that go into it. I agree, it is not elegant. On 8/8/2021 8:03 PM, Eszter Boros wrote: External Email - Use Caution Dear FreeSurfer Team, I am working on a longitudinal

Re: [Freesurfer] FreeSurfer questions exchange

On 8/9/2021 5:51 AM, 刘 亚飞 wrote: External Email - Use Caution Hello! In the process of learning freeSurefer, I have two questions: The first question is that I want to convert a file in .stl format to a .pial file, but the error "does not apear to be an STL file" appears when usin

Re: [Freesurfer] bbregister on DWI volumes using DOF 12 for epi distortions ?

Yea, I've tried that before. It does not work very well. You can proceed, but it will not be providing you with a very good correction. On 8/9/2021 9:30 AM, Shane Schofield wrote: External Email - Use Caution Hi Freesurfer Experts, I am trying to obtain coregister diffusion data b0 w

Re: [Freesurfer] longitudinal LME stats

On 8/11/2021 1:17 PM, Erik O'Hanlon wrote: External Email - Use Caution External Email - Use Caution Dear FS experts, I have run the longitudinal pipeline on a dataset with three timepoints. I am particularly interested in the longitudinal hippocampal and amygdala data and

Re: [Freesurfer] INSULA

We don't have post vs ant insula, but have you looked at the aparc.2009s.annot? It has a much finer insula segmentation. You might be able to merge some of those labels to get what you want. Otherwise, you can split the big insula label in the aparc with mris_divide_parcellation On 8/13/2021

Re: [Freesurfer] FreeSurfer qcache Inquiry

By default, the measure list includes the .K and .H files. You can specify your own list of measures with the -measure option. Eg, -measure thickness (you can add more -measure options for more measures) On 8/13/2021 5:10 PM, Junyeon Won wrote: External Email - Use Caution Dear Free

[Freesurfer] Setting up Freesurfer

External Email - Use Caution Hello, I was able to run Freesurfer before but when I try to source it now with the code source $FREESURFER_HOME/7.1.1/SetUpFreesurfer.sh I get the message: /Applications/freesurfer/7.1.1/SetUpFreeSurfer.sh:source:42: no such file or directory: /A

Re: [Freesurfer] LGI - trouble creating output file for each subject

It says that it cannot find /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white does that file exist and readable? On 8/17/2021 5:12 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caut

Re: [Freesurfer] FSFAST (mkcontrast-sess) with Octave

Hi Lauri, I was able to run this successfully here on 7.2. What version of FS are you using? Can you send /tmp/mkcontrast2.28236.m (if still there)? doug On 8/17/2021 3:10 PM, Lauri Tuominen wrote: > External Email - Use Caution > > Dear Surfers, > I am trying to run fsfast mkcontrast

Re: [Freesurfer] INSULA

External Email - Use Caution Thank you so much. We’ll try, Best, Elisabetta Sent from my iPhone On Aug 17, 2021, at 5:38 PM, Douglas N. Greve wrote: We don't have post vs ant insula, but have you looked at the aparc.2009s.annot? It has a much finer insula segmentation. You mi

Re: [Freesurfer] Setting up Freesurfer

External Email - Use Caution Hello Haley, You could try bringing up a new terminal window and then do the following, $ cd $HOME$ bash… output deleted …$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1 The ls command below should show you the two .sh files needed to setup the

[Freesurfer] 回复: FreeSurfer questions exchange

External Email - Use Caution Hello！ I mean if I only have reconstructed surface files such as ?h.pial or ?h.white, and want to perform cortical surface parcellation on them to generate label files and .annot files,how can I do it? Thank you! 发件人: Douglas N. Greve

Re: [Freesurfer] LGI - trouble creating output file for each subject

External Email - Use Caution Dear Dr. Douglas, Thank you so much for your response. I just checked in the surf folder of this specific subject and yes, rh.white does exist. Not 100% sure how to check if it's readable for freesurfer - could you please explain? Thank you! On Tue, A

[Freesurfer] Unsubscribe

External Email - Use Caution I've tried several times to unsubscribe from the mailing list. Please help, I'm inundated with emails that are no longer relevant to me. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://ma