[Freesurfer] mri_info orientation string ???

ue of "???". Would anyone correct or confirm my finding? Thank you! John Xiaojiang Yang <https://secure-web.cisco.com/1z35I78V94iRbbYPmh53mt00toQQUpCtob0Flq38T-DIF4eyYbMf_bMQ3sEmfHiyZWKybvM4YKjdzOzLJ9CYVa7B82DjIMljR_9yUKIr7uKGb8S4oCzCAmCmy7QYcYZLZZ-7xiq5cY6dhd3w4WwHj6

[Freesurfer] mri_info orientation string ???

External Email - Use Caution Dear Freesurfer Experts, I have a question regarding the orientation string gotten from mri_info. When I apply mri_info command to a DIOM series I generated programmatically, I get the "???" result, and hence primary slice direction is also unknown:

[Freesurfer] Capture multiple images using freeview

External Email - Use Caution Dear FS developers, I know how to use freeview to capture one static image and save it to a file. For example, I can capture coronal view's slice 100 using this command: freeview \ -v $SUBJECTS_DIR/$subjectid/mri/orig.mgz \ -f $SUBJECTS_DIR/$

Re: [Freesurfer] Cortical thickness on version 6 vs 7

for the HCP Pipelines for now. We usually quote 2.6mm average cortical thickness for young adults, but it does depend on age. Matt. From: on behalf of Xiaojiang Yang Reply-To: Freesurfer support list Date: Friday, March 12, 2021 at 10:29 AM To: Freesurfer support list Subject: [Freesurfer] Cortical

[Freesurfer] Cortical thickness on version 6 vs 7

External Email - Use Caution Dear Freesurfer developers, I have a cohort of subjects that are already run under FS 6. I recently upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects under FS 7. When comparing the cortical thickness results obtained from

[Freesurfer] Which pial surface to trust, with or without -FLAIR option

External Email - Use Caution Dear FS developers, I have run FS’s recon-all on many cases, with and without -FLAIR options. I found the pial surface results (?h.pial) I obtained without -FLAIR option fit to the original image (subjected/mri/orig.mgz) much better than those with

Re: [Freesurfer] How to do permutation for multiple comparison correction?

:47 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200804> There are actually only N-1 permutations that you can make: Real matrix: 1 0 0 1 0 1 0 1 0 1 Permutation 1: 0 1 1 0 0 1 0 1 0 1 Permutation 2: 0 1 0 1 1 0 0 1 0 1 On 8/4/2020 10:41 AM

Re: [Freesurfer] How to do permutation for multiple comparison correction?

1 0 1 0 1 0 1 ... n times you would then permute the design matrix On 7/23/2020 12:06 PM, Xiaojiang Yang wrote: External Email - Use Caution Hi Doug, For the first question, you answered "It is unusual, though it should work". Could you please briefly describe the way FS

Re: [Freesurfer] How to do permutation for multiple comparison correction?

search?l=freesurfer@nmr.mgh.harvard.edu=date:20200723> On 7/21/2020 11:45 AM, Xiaojiang Yang wrote: External Email - Use Caution Hi Doug, For your questions: 1. "Not sure what you mean by in the ROI. Are you trying to permute across space? That generally does not work because the points are no

Re: [Freesurfer] area.pial files for fsaverage

<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200723> Do you not see ?lh.pial.avg.area.mgh in $FREESURFER/subjects/fsaverage/surf ? On 7/21/2020 3:11 PM, Xiaojiang Yang wrote: External Email - Use Caution Dear FS developers, I have noticed that for

[Freesurfer] area.pial files for fsaverage

External Email - Use Caution Dear FS developers, I have noticed that for each subject, there are ?h.area and ?h.area.pial files under the $SUBJECT_DIR/$subject/surf sub-directory. According to Bruce's words from here

Re: [Freesurfer] How to do permutation for multiple comparison correction?

e if I should reject or accept null hypothesis based on cluster-wise significance level. What problems do you think I have in this idea? Thanks a lot! On 7/21/2020 1:12 AM, Xiaojiang Yang wrote: External Email - Use Caution Dear FS experts, Instead of using mri_glmfit-sim, I am tr

[Freesurfer] How to do permutation for multiple comparison correction?

External Email - Use Caution Dear FS experts, Instead of using mri_glmfit-sim, I am trying to implement a customized multiple comparison correction algorithm using permutation. Before I implement my own, I want to make sure my permutation idea is correct. So I was looking at how

Re: [Freesurfer] Compare individual to a group

mgh.harvard.edu=date :20200511> Mon, 11 May 2020 14:14:42 -0700 Just call your thickness file some other name, eg, lh.xformed.thickness.mgz, the just specify --meas xformed.thickness.mgz On 5/11/2020 3:52 PM, Xiaojiang Yang wrote: External Email - Use Caution Thank you Douglas! I

Re: [Freesurfer] Compare individual to a group

t, can then create an FSGD file with two classes as before but > no continuous variable. Then just have a contrast that computes the diff > between the patient and the mean of the controls. > > On 5/8/2020 11:49 AM, Xiaojiang Yang wrote: > > External Email - Use Caution > >

Re: [Freesurfer] Compare individual to a group

rom :%22Douglas+N.+Greve%22> Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date :20200507> Thu, 07 May 2020 14:56:08 -0700 sorry, please include the previous email chain so that I know what you are referring to On 5/7/2020 5:33 PM, Xiaojian

Re: [Freesurfer] Compare individual to a group

External Email - Use Caution Douglas, Just as I mentioned in the initial email, subjects in the healthy group have different ages. Because average cortical thickness is believed to be declined as the age gets older, I want to "normalize" the group by multiplying each subject's

Re: [Freesurfer] Compare individual to a group

External Email - Use Caution Hi Douglas, Thank you very much! Could you please help me with more detailed information? 1) Should I use "Variables age" or "Variables age weight" in the fsgd file? If I can use either of them, which one is better? 2) For the contrast

[Freesurfer] Compare individual to a group

External Email - Use Caution Dear FS experts, I have a group of healthy subjects. Given a new individual subject, I want to compare its cortical thickness to the healthy group so that I can find where the thickness is abnormal (thickening or thinning). I use fsaverage as the

Re: [Freesurfer] sig.cluster.summary and sig.cluster.mgh of mri_glmfit-sim

External Email - Use Caution Hi Douglas, Not only vertex 10738. For all vertexes listed in the summary file, they all have a very big Max value (absolute) that is out of the visual range. Please see the video I grabbed from my screen: https://imgur.com/a/kkSO7sT *Thank you for

[Freesurfer] sig.cluster.summary and sig.cluster.mgh of mri_glmfit-sim

External Email - Use Caution Hi FS developers, I have used mri_glmfit-sim to do multiple comparison like below: mri_glmfit-sim --glmdir lh.thickness.0.glmdir --cache 3 abs --cwp 0.05 --2spaces and in the lh.thickness.0.glmdir/group.diff directory, I got some output

Re: [Freesurfer] How is Total cortical gray matter volume calculated

External Email - Use Caution Ian, You can use the mris_anatomical_stats command with the -b option. E.g., mris_anatomical_stats -b subjectid lh will give you a tabular output containing the total gray matter volume in the 3rd column: 128449 86239 *243375 *2.588 0.876

Re: [Freesurfer] Does FS guarantee the same results if run several times?

External Email - Use Caution Thank you Douglas! In my case, two runnings were from Centos7 and Redhat7 respectively. Good thing is that the difference of the average thickness is small - it's 0.006 mm. Both lh and rh have 0.006 mm differences, but one's lh is thicker than the

Re: [Freesurfer] Does FS guarantee the same results if run several times?

External Email - Use Caution Hi Douglas, I checked the recon-all.log files for both, and found the difference - my mistake, one used FLAIR as extra input and the other did not. I did find another case that has two different results in two runnings. Both runnings have

Re: [Freesurfer] Does FS guarantee the same results if run several times?

External Email - Use Caution Thank you Douglas and Tashrif! Does this mean I should run recon-all for each subject several times, and compute the average to get the more reliable thickness? Can anyone else confirm this? Thanks! Xiaojiang

Re: [Freesurfer] Does FS guarantee the same results if run several times?

External Email - Use Caution No. I just checked, they are not identical. Although some of numbers are the same, many are different. Xiaojiang Are the other results identical? Eg, lh.aparc.stats? On 4/17/2020 10:49 AM, Xiaojiang Yang wrote: External Email

[Freesurfer] Does FS guarantee the same results if run several times?

External Email - Use Caution Dear Freeserfer developers, I have run recon-all for a bunch of subjects on the same machine for several times. When I use the "mris_anatomical_stats" to calculate the statistics (specifically, I am interested in average cortical thickness), I

[Freesurfer] Can I rename subject id safely?

External Email - Use Caution Dear FS developers, I have done some recon-all computing for a group of subjects, subject1, subject2, . , subjectn, and the results are in the $SUBJECTS_DIR directory: $SUBJECTS_DIR |_ subject1

[Freesurfer] Reducing FreeSurfer recon-all time

External Email - Use Caution Freesurfer experts: I know in my powerful Linux machine, recon-all needs about 10 hours to finish all computation. What is the possible way I can use to greatly reduce this computation time from 10 hours to, say 1-3 hours? Is Sun Grid Engine (SGE),

Re: [Freesurfer] Registration file types confusion

External Email - Use Caution Hi Douglas, The link you gave to me ( https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) has some information about .dat file, but no information about .lta file at all. I

[Freesurfer] Registration file types confusion

External Email - Use Caution Hi everyone, I am confused by the two types of registration files: .lta and .dat. .dat file is simpler and easier to understand. But for the .lta files, there seems to be no detailed explanation regarding it. Can anyone point out to me where can I

[Freesurfer] Skull-stripped brain for non-T1 image

External Email - Use Caution Hi everyone, Suppose I have run Freesurfer with respect to a subject using the T1 image, and I have gotten the skull-stripped brain image (brain.mgz) in the /mir directory. Now I have a non-T1 image of the same subject, say, the (T2)FLAIR series, and

[Freesurfer] Registration of DIR (Double Inversion Recovery) series

External Email - Use Caution Hi all, I want to register DIR (Double Inversion Recovery) series to T1 series using Freesurfer. I used the command line similar to that used for FLAIR registration: bbregister --s subject001 --mov

[Freesurfer] Coordinates transformation from conformed space to the original FLAIR image

External Email - Use Caution Hi everyone, I have used both T1 and (T2) Flair images as inputs to recon-all, and I have generated some coordinates (ROI) that I can transform to the original T1 images. Basically, I use the two matrixes obtained from the mri_info -- vox2ras