Re: [Freesurfer] Trac-All Error

External Email - Use Caution Hi Dr. Yendiki, Thanks! That fixed the issue I was having. Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri ___ Freesurfer

[Freesurfer] eTIV vs. manual ICV

External Email - Use Caution I was just wondering if using the eTIV from FS 6.0 is a reliabile measure for intracanial volume normalization. Typically, manual ICV includes extra-axial CSF which I don't think is included in the eTIV method, correct? Our population is a control

Re: [Freesurfer] -bash: segmentThalamicNuclei.sh: command not found

Hi Veronica Did you source FreeSurfer? After that, the command would be: segmentThalamicNuclei.sh A7 /Users/vp/freesurfer/ANALISI_DATA/ Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Parisi

[Freesurfer] -bash: segmentThalamicNuclei.sh: command not found

External Email - Use Caution Dear Freesurfer Support Team, I'm trying to run the segmentThalamicNuclei.sh to segment the thalamic nuclei on a subject. I am using the latest Freesurfer dev version (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/). I previously ran

Re: [Freesurfer] [External] Freesurfer Digest, Vol 194, Issue 24

g the same error message saying that I should > > add the flag -cw256. Am I setting this option incorrectly? I am using > > freesurfer version 6.0.0. > > > > Thank you! > > Soichi Hayashi > > Screenshot from 2020-04-17 12-28-01.png > > > > > > > > &g

[Freesurfer] Which autorecon uses -hippocampal-subfields flags?

Douglas, Let's try with an example. See the two ways T2 image can be integrated with recon-all Altogether: recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all autorecon3 only: recon-all -subject

Re: [Freesurfer] Data on the Freesurfer surface

External Email - Use Caution Please ignore my last email. I added --out_type mgh and also changed the --out to end with ?h.mgh and it's done the trick. Please do let me know if this isn’t correct though! Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and

Re: [Freesurfer] Data on the Freesurfer surface

External Email - Use Caution Sorry, just to follow up on this. The surface based analysis needs the outputs in the format of MGH. I fear I may have missed a step here. Any advice would be great. Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision

Re: [Freesurfer] Data on the Freesurfer surface

External Email - Use Caution Great, thanks for this. Am I right in thinking that the only outputs from this command are COR-.info and COR-001 and that neither of these should have which hemisphere it was created from in their name? I also notice the examples on the wiki page

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

I don't understand the question. To run recon-all through to the end implies that you have run all the -autorecons On 4/17/2020 2:53 PM, Billah, Tashrif wrote: Right, I understand the rule about the scripts. However, my original question was about the subfields

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

External Email - Use Caution Hi Xiaojiang, Given the precision of MRI scanners, I would say it's safe to assume that this difference can be ignored. Best, Tim > On April 17, 2020 at 9:02 PM Xiaojiang Yang wrote: > > > External Email - Use Caution > > Thank

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] Which autorecon uses -hippocampal-subfields flags?

Right, I understand the rule about the scripts. However, my original question was about the subfields -hippocampal-subfields-T1/T2/T1T2 Again, can they be run with any of the autorecons separately? The example shown here

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

I think recon-all should be deterministic for multiple threads. I know that different machines can give different answers (but usually this is a mac vs linux thing). On 4/17/2020 2:34 PM, Xiaojiang Yang wrote: External Email - Use Caution Hi Douglas, I checked the recon-all.log

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

You have to run recon-all all the way through and then run the subfield scripts separately. On 4/17/2020 12:21 PM, Douglas N. Greve wrote: None! You have to run it all the way through to the end and then run them from the command line. On 4/17/2020 11:40 AM, Billah, Tashrif wrote: Hi all,

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] Which autorecon uses -hippocampal-subfields flags?

Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif . ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] convert gii to mgh/nii.gz (freesurfer surface)

External Email - Use Caution You will need to convert it to FreeSurfer surface format (instead of MGH/NIFTI, which are volume formats), the standard one is the binary surface format. Assuming your file is 'lh.white.gii': mris_convert lh.white.gii lh.white or to use the less

Re: [Freesurfer] Data on the Freesurfer surface

That looks good. The only thing to change is to specify the projection fraction for vol2surf to --projfrac 0.5 (so that it samples in the middle of the cortical ribbon rather than at the white/gray boundary) On 4/17/2020 1:36 PM, Mason Wells wrote: > External Email - Use Caution > >

Re: [Freesurfer] Data on the Freesurfer surface

External Email - Use Caution Hi, Can I just double check this seems correct to you experts? I am not 100% proficient in Freesurfer/FSL. I ran: bregister --s S1 --feat Data/Feat2/LM/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/ Which seemed to give me what I needed,

Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

External Email - Use Caution Just a quick follow up, I've now been able to find my issue in the wild as well (not just on my own machines). I use Arch Linux personally and on a small handful of workstations professionally, and when investigating using FS on Arch, I stumbled

Re: [Freesurfer] Data on the Freesurfer surface

Yes, use the template.nii.gz as the registration target. A long time ago we used to have some wrappers that would operate directly on feat folders. Not sure if they still work but, check out https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer On 4/17/2020 10:43 AM, Mason

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

thickness? Can anyone else confirm this?  Thanks! Xiaojiang Billah, Tashrif <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Billah%2C+Tashrif%22>Fri, 17 Apr 2020 08:34:14 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

None! You have to run it all the way through to the end and then run them from the command line. On 4/17/2020 11:40 AM, Billah, Tashrif wrote: Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags? autorecon1, 2 , or 3? My

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

When we run repeated analyses on the same data on the same system, we always get the same results doug On 4/17/2020 11:32 AM, Billah, Tashrif wrote: Hi Xiaojiang and Douglas, I think it is the attribute of having random initialization in the registration steps. This slight discrepancy can

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

Can you send the recon-all.log files for two of the runs that should be identical? On 4/17/2020 11:15 AM, Xiaojiang Yang wrote: 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

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

ail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from :%22Billah%2C+Tashrif%22> Billah, Tashrif <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date :20200417> Fri, 17 Apr 2020 08:34:14 -0700 Hi Xiaojiang and Douglas, I think it is the attribute of h

[Freesurfer] Which autorecon uses -hippocampal-subfields flags?

Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags? autorecon1, 2 , or 3? My goal is to use the flag specifically with one of the three and not with recon-all in general as shown in the above page. I do understand that the

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

Hi Xiaojiang and Douglas, I think it is the attribute of having random initialization in the registration steps. This slight discrepancy can also be observed with antsRegistration. I don't know the exact algorithm FreeSurfer uses for registration though. Best, Tashrif

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

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

Are the other results identical? Eg, lh.aparc.stats? On 4/17/2020 10:49 AM, Xiaojiang Yang wrote: 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

Re: [Freesurfer] concatenate transformations

If these are tkregister style .dat files, you can try mri_matrix_multiply On 4/16/2020 11:27 PM, Sam W wrote: External Email - Use Caution Hello! I performed two registrations: diffusion-to-orig.dat and orig-to-rawavg.dat. Now I would like to concatenate the two transformation

[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

Re: [Freesurfer] Data on the Freesurfer surface

External Email - Use Caution Great, thanks again Bruce. Doug, can you confirm this is the process for taking a filtered_func file and getting it onto the freesurfer surface ready for analysis? Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff

Re: [Freesurfer] Data on the Freesurfer surface

oh, then you probably want to use bbreg to register it and mri_vol2surf to sample it onto the surface. Doug is the expert on this and can add/correct if this is not the whole story :) cheers Bruce On Fri, 17 Apr 2020, Mason Wells wrote: External Email - Use Caution Hi Bruce, The

Re: [Freesurfer] Data on the Freesurfer surface

External Email - Use Caution Hi Bruce, The only pre-processing I have done is the motion correction, high pass filtering and distortion correction. So, as far as I know it is still in the volume and in the original functional space. Best wishes, Mason Mason T Wells, MSc PhD

Re: [Freesurfer] Data on the Freesurfer surface

Hi Mason is your filtered_func file already sampled onto the surface or is it a volume? cheers Bruce On Fri, 17 Apr 2020, Mason Wells wrote: External Email - Use Caution Hi all,    I am trying to use an analysis package that works on surface based data (SamSrf). I have

Re: [Freesurfer] convert gii to mgh/nii.gz (freesurfer surface)

Hi Marina can you include command line and full screen output (in text!) so we can understand what you mean by "it doesn't work". Also, note that .mgh/.nii.gz are volume formats, not surface ones, so you can't convert a surface to them. You will need to use our surface format cheers Bruce

[Freesurfer] Data on the Freesurfer surface

External Email - Use Caution Hi all, I am trying to use an analysis package that works on surface based data (SamSrf). I have ran Feat and have a filtered_func file which is of course the motion corrected/unwarped version of my EPI. However, I need some advice on how to get

[Freesurfer] convert gii to mgh/nii.gz (freesurfer surface)

External Email - Use Caution Hi experts, How can I convert a surface in .gii format to a surface in .mgh or nii.gz format? I tried with mris_convert but it doesn't work. Best regards, Marina ___ Freesurfer mailing list