[Freesurfer] Reconall with no-MPRAGE T1w image?

2019-09-03 Thread Rovai Antonin
External Email - Use Caution Hello, From the ReconAllTable (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see that the mri_normalize step (producing the T1.mgz file) has the -mprage option. I have two questions: 1. What is this option doing exactly?

[Freesurfer] Question about how to build .gca files from non-human atlas and images

2019-09-03 Thread arsene ella
External Email - Use Caution *Dear **Freesurfer experts,* *I’ve built an atlas of structures of a non-human average brain and now **I would like to build **its** .gca files from scratch. **From the Freesurfer mailing list, I saw that this is possible using **rebuild_gca_atlas.csh*

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-03 Thread Rovai Antonin
External Email - Use Caution Hey So opening only the conformed image in freeview, mricro and fsleyes constantly gives me crazy results. Also, the wm segmentation is completely wrong so I really think there something wrong in the file…. Best Antonin Hôpital Erasme - ULB

Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

2019-09-03 Thread Bruce Fischl
Hi AR 1. mprage in general has higher CNR and lower SNR than non inversion-prepared T1w sequences like FLASH. THe -mprage switch takes advantage of this to loosen the intensity gradient threshold in the region filling of the wm. 2. If you just leave out the -mprage switch it will revert to

[Freesurfer] mri_surf2surf without sphere.reg

2019-09-03 Thread Caspar M. Schwiedrzik
External Email - Use Caution Hi! I am having some issues projecting retinotopic mapping data from a monkey analyzed in surface space onto its surface using rtview. The issue seems to be that the data need to be converted into paint format through mri_surf2surf, and that we do not

Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

2019-09-03 Thread Bruce Fischl
oh, I see. Yes it is defaulted to being on in recon-all. You can specify -no-mprage to recon-all to turn it off, although it might be worth trying both out on a set of subjects and seeing which does a better job cheers Bruce On Tue, 3 Sep 2019, Rovai Antonin wrote: External Email

Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

2019-09-03 Thread Rovai Antonin
External Email - Use Caution Hi Bruce, Thanks for your response. From what I read on the wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) the switch in on by default since freesurfer6.0 (but that doesn’t seem to be the case in 5.3). At any rate we use

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-03 Thread Bruce Fischl
Hi Antonin hmmm. Can you try *only* loading the conformed image and seeing how it looks? freeview will use one of the images as the basis for it's display coordinates, which can cause apparent slicing artifacts that are only display issues for other volumes. cheers Bruce On Tue, 3 Sep

Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

2019-09-03 Thread Rovai Antonin
External Email - Use Caution (Continued) Of course I meant using the recon-all command! On 3 Sep 2019, at 15:48, Rovai Antonin mailto:antonin.ro...@erasme.ulb.ac.be>> wrote: External Email - Use Caution Hi Bruce, Thanks for your response. From what I read on the

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-03 Thread Bruce Fischl
hmmm. Can you tar and gzip the whole subject dir and upload it to our ftp site? On Tue, 3 Sep 2019, Rovai Antonin wrote: External Email - Use Caution Hey So opening only the conformed image in freeview, mricro and fsleyes constantly gives me crazy results. Also, the wm segmentation

Re: [Freesurfer] qdec contrast and data extraction

2019-09-03 Thread Greve, Douglas N.,Ph.D.
You might have done something wrong along the way. When you run the montecarlo correction, it will create a file with the thickness values in it for each cluster. the first thing to do is to load that and see if you see the expected differences. The other thing is to not go back into native

[Freesurfer] Extracting contrast data from mri_glmfit to graph

2019-09-03 Thread cody samth
External Email - Use Caution Hello, I have a question regarding how to graph results that came from a vertex wise analysis using the command mri_glmfit and mri_glmfit-sim. I was interested in investigating an interaction effect between groups and my variable of interest

Re: [Freesurfer] mri_surf2surf without sphere.reg

2019-09-03 Thread Greve, Douglas N.,Ph.D.
Yes, just specify --surfreg white (or some other surface you do have). On 9/3/2019 9:51 AM, Caspar M. Schwiedrzik wrote: External Email - Use Caution Hi! I am having some issues projecting retinotopic mapping data from a monkey analyzed in surface space onto its surface using rtview.

Re: [Freesurfer] Compare vertexwise correlation maps

2019-09-03 Thread Greve, Douglas N.,Ph.D.
You want to see if the correlation values themselves? You can't do that (unless you have a bunch of correlation maps). You have to incorporate your question/hypothesis into the design and contrast. On 9/2/2019 11:14 AM, Matthieu VANHOUTTE wrote: > External Email - Use Caution > > Dear

[Freesurfer] Problem with lGI

2019-09-03 Thread Avi Gharehgazlou
External Email - Use Caution Hi, I have ran the lGI flag many times in the past. However, now that I am trying to run the flag on a new group of participants I get the below error. Will you please tell me how I can fix this? Thanks so much, Avi New invocation of recon-all

Re: [Freesurfer] mri_surf2surf without sphere.reg {Disarmed}

2019-09-03 Thread Caspar M. Schwiedrzik
External Email - Use Caution Thanks Doug, that worked! Caspar Am Di., 3. Sept. 2019 um 17:03 Uhr schrieb Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu>: > Yes, just specify --surfreg white (or some other surface you do have). > > On 9/3/2019 9:51 AM, Caspar M. Schwiedrzik

[Freesurfer] make_average_subject error

2019-09-03 Thread Maxime Perron
External Email - Use Caution ​Dear Freesurfer Experts, I have the following issue when running the make_average_subject command ( make_average_subject --subjects (Subjid) --out BrainaverageN72) :  Building hash of lh white Building hash of lh pial Building hash of

Re: [Freesurfer] Compare vertexwise correlation maps

2019-09-03 Thread Matthieu Vanhoutte
External Email - Use Caution So if I obtained two correlation maps from the same population but based on different input parameters, how could I demonstrate that vertex correlation values are statistically « strongest »/« lowest » in one of the map compared to the other ?

[Freesurfer] (Revised) Clusterwise correction for multiple comparisons

2019-09-03 Thread Gwang-Won Kim
External Email - Use CautionHi there, To perform a cluster-wise correction for multiple comparisons, I ran monte carlo simulation as follows: mri_glmfit-sim --glmdir g1v2.wls --3spaces --grf  2 abs I know that "- -3spaces" means adjusting p-values for both hemispheres and

[Freesurfer] Clusterwise correction for multiple comparisons

2019-09-03 Thread Gwang-Won Kim
External Email - Use CautionHi there, To perform a cluster-wise correction for multiple comparisons, I ran monte carlo simulation as follows: mri_glmfit-sim --glmdir g1v2.wls --3spaces --cache 2 abs I know that "- -3spaces" means adjusting p-values for both hemispheres and

[Freesurfer] qdec contrast and data extraction

2019-09-03 Thread Maximo, Jose Omar
External Email - Use Caution Hi, Which specific file should I load? I see cluster.mgh, cluster.summary, sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and pdf.dat. How can I extract the values from fsaverage space? Basically, what is the correct way to extract values from these

[Freesurfer] issue with lesions

2019-09-03 Thread Sam W
External Email - Use Caution Hello, I have run recon-all on T1 scans of patients with WM lesions. I noticed however that for some patients the lesion is excluded from aparc.a2009s+aseg.mgz but for other patients it is included (and labelled as non-lesion). Ultimately I'd like to