Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi Andrew, My test in December with last version of make_average_surface worked correctly. However, now I am trying to make another average subject and medial_wall.label is not created. I am using the last patch as last time. It is unusual because last time label folder was correctly created. I

[Freesurfer] Freesurfer longitudinal templates failed - time points from different scanners

Dear experts, I run FreeSurfer 6.0 longitudinal pipeline on a set of scans acquired with identical protocol (ADNI) but 2 different Philips 3T scanners (all time 1 with Achieva, all time 2 with Ingenia). Unfortunately ~ 50% of the within-subjects templates completely failed. Is there anything I

[Freesurfer] corRead(): can't open file /home/andraderenew/COR-.info

Hello: I run the command to open freeview -v…(the installation guide example in Bert) and I get the error in I point out in the subject of this email. Thanks for the help in advance! Sincerely, Rene Andrade. ___ Freesurfer mailing list Freesurfer@nmr

[Freesurfer] motion parameter in preprocessing stream

Dear all FreeSurfer users, I was wondering if I can extract any parameter of movement from the recon-all processing using FreeSurfer 5.1. Thanks in advance! Kind regards, Carme ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed if you tar, gzip and ftp this subject to our ftp site we will take a look cheers Bruce On Thu, 18 Jan 2018, m.ba...@uliege.be wrote: Dear Bruce, Attached is the screen shot of the results of the segmentation of the perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the

[Freesurfer] mri_em_register and mri_ca_register

Dear Freesurfer community, I would like to get a better sense of how mri_em_register and mri_ca_register work. I understand the former is a linear registration and the latter is nonlinear, and that they are both meant to register an individual to a template space (MNI152?). Would it be possib

Re: [Freesurfer] recon-all exited with error

Hi Andrew Thank you for your response. I gave it a go and still no luck, unless I am missing something completely obvious here trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anon

Re: [Freesurfer] mri_em_register and mri_ca_register

Hi Ruy they both register to a .gca atlas that is quite a bit more accurate than the MNI. The details are in the 2002 and 2004 papers. cheers Bruce On Thu, 18 Jan 2018, Ricardo Valle wrote: > Dear Freesurfer community, > > I would like to get a better sense of how mri_em_register and mri_ca_re

Re: [Freesurfer] mri_em_register and mri_ca_register

I see. Thank you very much! Cheers, Ruy > On Jan 18, 2018, at 1:24 PM, Bruce Fischl wrote: > > Hi Ruy > > they both register to a .gca atlas that is quite a bit more accurate than > the MNI. The details are in the 2002 and 2004 papers. > > cheers > Bruce > On Thu, 18 Jan 2018, > Ricardo Valle

Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

I've uploaded the data. Just want to confirm you received it. Thanks, Carissa From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Saturday, January 13, 2018 3:49 PM To: Freesurfer support list Subject: Re: [Freesurf

Re: [Freesurfer] Visualisation left and right hemisphere

Hi Ahmad, you can use mris_left_right_register to register the left and right hemis, then mris_apply_reg to map the left annot to the right (or other way around). ps. please remember to post to the FS list. Thanks! On 1/17/18 9:13 AM, Ahmad Mheich wrote: /Hello, / // /Is it possible to combi

Re: [Freesurfer] why freesurfer is not able to segment frontal cortex

Use aparc+aseg.mgz On 1/12/18 5:14 AM, Vidhu Agrawal wrote: Does freesurfer segments frontal cortex? If yes the how we can do that I have tried to do it by using the command :mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_superior.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-s_fron

Re: [Freesurfer] ROI statistics and median values

I don't think we have anything. You can do it in matlab, eg aseg = MRIread('aseg.mgz'); vol = MRIread('vol.nii.gz'); ind = find(aseg.vol==17); % left hippo median(vol.vol(ind)) On 1/12/18 10:42 AM, Helen Beaumont wrote: > I can use mri_segstats to get mean and std dev for values within a > s

Re: [Freesurfer] Jittering Fixation Time

That is fine On 1/12/18 2:26 PM, Ashley Cole wrote: Dear FreeSurfer Experts, I have a question about jittering the fixation point and how Freesurfer handles it. Is it ok to have different rest times in the paradigm file for FS-FAST pipeline? In the paradigm file, I am giving it an actual o

Re: [Freesurfer] Using subject specific template, atlas, & TPM

you can use gcatrain (and jkgcatrain for testing) if you are using v6 On 1/12/18 3:27 PM, Bruce Fischl wrote: Hi Ramesh if you have segmentations in our aseg format (or edited asegs for that matter if you find them not accurate enough), you should be able to use mri_ca_train to genenerate a

Re: [Freesurfer] aparcstats2table

Why don't you just create a fake directory structure. Should be pretty easy to script (if you know how to script:) On 1/15/18 3:44 AM, Stephanos Leandrou wrote: Dear Freesurfer Developers, I want to use the asegstats2table and aparcstats2table for my research. First of all, my subjects (sev

Re: [Freesurfer] motion parameter in preprocessing stream

I don't think so, sorry On 1/18/18 8:58 AM, Carme Uribe Codesal wrote: Dear all FreeSurfer users, I was wondering if I can extract any parameter of movement from the recon-all processing using FreeSurfer 5.1. Thanks in advance! Kind regards, Carme ___

[Freesurfer] PET partial volume correction

Dear Dr Greeve, I interestingly read the manuscript "Different partial volume correction methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank you for publishing this data. I understood from this paper that he recommended stream for PVC is to correct the PET images using

[Freesurfer] mri_coreg

Dear FS developers, Are there any versions of "mri_coreg" that allows to output the registered images. I mean flag "--out or -o" similar to spmregister? Thanks for any guidance John___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.

Re: [Freesurfer] mri_coreg

No, sorry. You have to use mri_vol2vol. Should be pretty simple On 1/18/18 4:34 PM, John Anderson wrote: Dear FS developers, Are there any versions of "mri_coreg" that allows to output the registered images. I mean flag "--out or -o" similar to spmregister? Thanks for any guidance John

Re: [Freesurfer] PET partial volume correction

It is volume-based for subcortical On 1/12/18 8:17 AM, John Anderson wrote: Dear Dr Greeve, I interestingly read the manuscript "Different partial volume correction methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank you for publishing this data. I understood from

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

Is the problem that the surfreg command is failing or that you don't know how to apply LME? On 1/17/18 9:55 AM, lanbo Wang wrote: Hi Martin, I didn't try to run recon-all, I try to run flipped. The code I used is: foreach subject (subj_27_2.long.s27_base) foreach?   surfreg --s $subject --t f

Re: [Freesurfer] PET partial volume correction

Dear Dr Greve, Thank you so much for the quick response. Just to confirm that I understood the procedure correctly. The analysis is volume based (i.e. voxel-wise) for the subcortical structures using mask created by freesurfer's "mri_binarize" for these regions. Correct? Original Mess

Re: [Freesurfer] PET partial volume correction

It is a little tricky because you don't want to use different masks for different subjects. I recommend using CVS where I've created a subcoritcal mask in 2mm space (mri.2mm). So the idea would be that you map your subcortical MG map to CVS space, then smooth it (mri_fwhm) specifying the subcor

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Why are you doing your own MC simulation? You can just use the tables that we distribute ... On 1/17/18 6:12 PM, miracle ozzoude wrote: Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswik

[Freesurfer] Hippocampal subfield segmentation with T1 and T2

Hi all, I've been trying to run the hippocampal subfield segmentation with T1 and T2 images, and haven't had much luck. I had previously run recon-all on all my scans in v5.3, but testing on one subject I re-ran recon-all with the additional T2 scan, and that seems to have run fine. However, when

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Hello Doug, Thanks for responding. I am running a whole brain analysis as result shouldn’t I build my own MC simulation? Best, Paul Sent from my iPhone > On Jan 18, 2018, at 5:23 PM, Douglas Greve wrote: > > Why are you doing your own MC simulation? You can just use the tables that we > d

Re: [Freesurfer] Using subject specific template, atlas, & TPM

Dear Bruce and Douglas, Thank you for your suggestions. I am trying it and will need your suggestions on result. Thank you Ramesh On Fri, Jan 19, 2018 at 2:08 AM, Douglas Greve wrote: > you can use gcatrain (and jkgcatrain for testing) if you are using v6 > > On 1/12/18 3:27 PM, Bruce Fischl w

Re: [Freesurfer] Hippocampal subfield segmentation with T1 and T2

Hi Cassie, It seems to be a problem with mri_robust_register, when trying to allíen the t1 and t2 scans. Martin, any ideas? Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Cassandra Wannan Sent: Th