Re: [Freesurfer] Problem with recon-all command in tutorial dataset

External Email - Use Caution Try: export TUTORIAL_DATA=/home/shao/tutorial_data Tim > On August 11, 2020 at 6:51 AM Wei Shao wrote: > > > External Email - Use Caution > > Hi, Freesurfer Team > > My name is Wei Shao, I just a beginner of Freesurfer. As I play

[Freesurfer] Problem with recon-all command in tutorial dataset

External Email - Use Caution Hi, Freesurfer Team My name is Wei Shao, I just a beginner of Freesurfer. As I play around with the tutorial data, here is a problem I met, I tried to recon-all the dicoms data as the tutorial instruction practice with the date instructed, but it alway

[Freesurfer] Local GI error with Matlab

External Email - Use Caution Dear Freesurfer experts, Hope you are all safe and well. I changed the version of the matlab that I was using (from 2020a to 2019b) and most errors that I was having were fixed after running the LGI command. The only issue that I'm still having is the

Re: [Freesurfer] Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Medial Nucleus Errors

External Email - Use Caution Hi Eugenio, Happy to share that with you. I am pretty new to Freesurfer, so could you clarify what volumes you would like me to share? I currently have "aseg.mgz", "rh.hippoAmygLabels-T1.v21.FS60.mgz", "lh.hippoAmygLabels-T1.v21.FS60.mgz", and "nu.m

Re: [Freesurfer] Thalamic nuclei in FSL

External Email - Use Caution Hi Doug, That would do it. Thanks! However, I ran bbregister, got out the register.dat file, input that into the vol2subfield command and now it’s giving me an error stating: "dst or src volume is invalid. Inverse likely wrong…error: mir_concatenate_

Re: [Freesurfer] Question about obtaining stats from a gtm file

Download and try this program https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table I wrote it 3 years ago but somehow it did not make it into the distribution. I'm not sure it works, so let me know how it goes On 8/10/2020 1:09 PM, Gary Tan wrote: External Email - Use Cauti

Re: [Freesurfer] Freesurfer Digest, Vol 198, Issue 18

avarro-Cebrian, PhD.* > > > Assistant Research Scientist > > > Psychological and Brain Sciences Department > > > Johns Hopkins University > > > > > > ___ > > > Freesurfer mailing

[Freesurfer] Question about obtaining stats from a gtm file

External Email - Use Caution Hi freesurfer mailing-list, I am trying to use asegstats2table to combine the individual gtm.stats.dat files. I assume that the output is mixed up because these gtm files have no column labels. Below is the command I used: asegstats2table --inputs

Re: [Freesurfer] Freesurfer Digest, Vol 198, Issue 18

rsity > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- next part -- > An HTML attachment was scrubbe

Re: [Freesurfer] img (with ifh header) to mgz

what is ifh? Interfile? I don't know how to convert ifh On 8/10/2020 10:57 AM, Ana Navarro Cebrian wrote: External Email - Use Caution Hi all, How can I view an .img or convert it to .mgz? I've used .img files with freesurfer, but their headers had a .hdr extension. In this case, th

[Freesurfer] img (with ifh header) to mgz

External Email - Use Caution Hi all, How can I view an .img or convert it to .mgz? I've used .img files with freesurfer, but their headers had a .hdr extension. In this case, the header has an .ifh extension and I'm not able to view the image in freesurfer. Thanks! -- *Ana Nava

Re: [Freesurfer] high pass filter cutoff

Oh, Sorry, it chould probably have been .0313Hz. Assuming that it is 16 sec on and 16 sec off, then the period is 32 sec. 1/32sec = .0313Hz On 8/7/2020 11:29 AM, Nasiriavanaki, Zahra wrote: > Could you please explain how you came up with “0.0625 Hz”? > You mentioned in your first email: “With a b

[Freesurfer] Mean curvature comparison

External Email - Use Caution Hi, I want to compare mean curvature between groups on QDEC using the “curv” measure. I've learned from the archives that FreeSurfer calculates numerous curvature-based functions by default in the recon stream and stores them in the “surf” directory. I

[Freesurfer] Skull strip t1 in recon-all

External Email - Use Caution Dear freesurfer team I'm trying to use my own skull stripped T1 when running recon-all. For this, I'm doing following steps: 1) run recon-all with -autorecon-1 -noskullstrip 2) mri_convert --in_type nii --out_type mgz -rl ./FreeSurfer/ID/mri/orig.mgz -

Re: [Freesurfer] Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Medial Nucleus Errors

Dear Angel, It’s hard to tell without seeing the segmentation in 3D. Would you mind sharing, please? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Angel Hammond Reply-To: Freesurfer support l

Re: [Freesurfer] Comparing surface maps

Try this To regress include a per-vertex regressor (PVR, --pvr) in mri_glmfit. This procedure will essentially add a column to the design matrix for each vertex. Eg, if your FSGD file (my.fsgd) has two groups, then, by itself, the design matrix would be two columns, one for each group. You will

Re: [Freesurfer] cortical surface area calculation

Yes, it will On 8/7/2020 6:27 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi all, Does this command  calculate the Cortical Surface Area without the non-cortical Medial Wall?? mris_calc --label ../label/lh.cortex.label lh.area stats Jim

[Freesurfer] Hippocampus_substructures_normalization

External Email - Use Caution Hi. team! Recently, I submitted a paper dealing with volumes of hippocampus and its subfields in epilepsy patients who have significantly reduced hippocampal volume (compared with normal controls) and, in that paper, I used the normalization method u

Re: [Freesurfer] Recon-all Soft Errors

You can use https://gate.nmr.mgh.harvard.edu/filedrop2/ to upload your file. Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Elana Sarabin Sent: Sunday, August 9, 2020 11:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] Recon-all Soft