Re: [Freesurfer] Cortical surface

External Email - Use Caution OK. Thank you very much. Sincerely, Zheng At 2018-08-13 01:15:26, "Douglas Greve" wrote: You can break up the aparc annotation into labels (mri_annotation2label), then create a new annotation with just the insula (mris_label2annot) On 8/12/

Re: [Freesurfer] Stats2table_bash.sh script

External Email - Use Caution Thanks Robert, I guess my main issue is that I don't fully understand how the script works: [1] export SUBJECTS_DIR=*$PWD* *[2] list="`ls -d */`"* [3] asegstats2table --subjects *$list *--meas volume --skip --statsfile wmparc.stats --all-segs --tablef

Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files

oh, maybe we never got around to writing a write_patch.m. We'll put one together and send it to you Bruce On Sun, 12 Aug 2018, Dinicola, Lauren wrote: Hi Dr. Fischl, Thank you so much for this response. This is a great idea, but I have not yet been successful with writing out the adjusted stru

Re: [Freesurfer] Stats2table_bash.sh script

Hello K, If you type $ asegstats2table --help you will see that you can specify subjects on the command line as, e.g., for bert as —subjects bert or apparently -s bert It looks like the subjects option expects the name for at least one subjects (data), but the help output says you can list m

Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files

Hi Dr. Fischl, Thank you so much for this response. This is a great idea, but I have not yet been successful with writing out the adjusted structure to a ?h.cortex.flat.patch file. Is there a specific command for writing a patch? Thank you again, Lauren On Wed, Aug 8, 2018 at 3:04 PM, Bruce Fis

Re: [Freesurfer] Stats2table_bash.sh script

Hello K, If you type $ asegstats2table --help you will see that you can specify subjects on the command line as, e.g., for bert as —subjects bert or apparently -s bert It looks like the subjects option expects the name for at least one subjects (data), but the help output says you can list m

Re: [Freesurfer] T1 mapping

On 8/10/18 3:26 PM, Fotiadis, Panagiotis wrote: 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 MA

Re: [Freesurfer] Plotting QDEC results

On 8/11/18 12:02 PM, Avi Gharehgazlou wrote: External Email - Use Caution Thank you for your reply. I chose the 1.3 threshold based on LGI papers in the ASD literature, but I will use 2.0. 2 is still too low. You'd need at least 3. 1. By permutation do you mean FDR correction? no

Re: [Freesurfer] coregistering with bbregister

On 8/10/18 6:48 PM, Ben M wrote: 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 f

Re: [Freesurfer] Cortical surface

You can break up the aparc annotation into labels (mri_annotation2label), then create a new annotation with just the insula (mris_label2annot) On 8/12/18 5:17 AM, 郑凤莲 wrote: External Email - Use Caution Dear experts,   I an using FS 6.0 for cortical reconstructions.  I can show whol

[Freesurfer] Stats2table_bash.sh script

External Email - Use Caution Hi, I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & Dr. Vanessa Sluming. And I get This error: File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJEC

[Freesurfer] Cortical surface

External Email - Use Caution Dear experts, I an using FS 6.0 for cortical reconstructions. I can show whole brain regions (tksurfer...), as shown in the picture. However, I just want to show insular region. Is there any way to complete it? I am looking forward to your reply.