[Freesurfer] KWWidgets

A FreeSurfer build from source requires KWWidgets, but it has been deprecated for 10 years. What does Freesurfer use this code for? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Creating ROI on the functional map

It doesn't work on tksurfer. But it's ok. So Doug, is this the latest tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview for FS-FAST and creating functional ROI? More specifically, do I need to use "mri_vol2surf" to get the activation on the surface?

Re: [Freesurfer] aseg and aparcstats2table on longitudinal data

I don't know about #1 (I think not). For #2 you shold use the subject names from the longitudinal analysis On 02/26/2018 11:39 AM, Lisa Delalande wrote: > Hi FreeSurfer experts, > > I would like to use the asegstats2table and the aparcstats2table > commands on my longitudinal data, that have

Re: [Freesurfer] questions about the segamentation volume

You should check the accuracy of the segmentations in a few of the outlier subjects On 02/26/2018 03:18 PM, Ting Li wrote: > Hi FreeSurfer Expert, > > I followed the Anatomical ROI analysis tutorial and make a > aseg.vol.table for the 40 subjects. However, the segment volume can > various a

Re: [Freesurfer] FSGD and Contrast to determine the effect of age on performance

You would keep both Perform and Age in addition to adding Perform*Age. I would first use DODS to test for a difference between groups in the Perform*Age variable [0 0 0 0 0 0 1 -1]. If there are no differences, then use DOSS to test for an effect of Perform*Age [0 0 0 0 1]. On 02/26/2018

Re: [Freesurfer] FSGD and Contrast to determine the effect of age on performance

Thanks much Dough for your reply. So if I add another column Performance*Age (after removing the mean of each) in my fsgd file (and remove individual columns for Performance and age), could you please tell what will be the contrast matrix (after only Gender as a covariate) in that case i.e. for

Re: [Freesurfer] FSGD and Contrast to determine the effect of age on performance

On 02/24/2018 12:00 AM, Martin Juneja wrote: > Hi experts, > > I am not sure if this has already been addressed in FS discussion. > > If my fsgd file looks like following: > > Class Male > Class Female > Variables Performance Age > Input S1 Male 181 25 > Input S2 Female 167 23 > > > >

Re: [Freesurfer] Creating ROI on the functional map

I think it should work; We are not using tksurfer any more (freeview instead), but I think it should still work On 02/23/2018 05:16 PM, Sarah Cole wrote: > Hi, > > I was wondering if this method is still applicable in version 6 > https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs > > > I

Re: [Freesurfer] Unknown Label in following postprocessing with mne-python

I'm not sure I understand what you are asking about. Do you mean in the aseg.mgz or the aparc+aseg.mgz? Unknown is usually just stuff outside of the head, but sometimes can be in the head (eg, with aparc+aseg.mgz). On 02/22/2018 08:51 AM, Daniel van de Velden wrote: > Dear fellow colleagues, >

Re: [Freesurfer] Extraction of cortical thickness in native space

Can you be more specific about which step is failing and how you are verifying the failure? On 02/21/2018 05:21 PM, Albrecht, Daniel S. wrote: > > Hello, > > > We are attempting to extract cortical thickness values from a > pre-defined ROI in MNI space. > > > Originally, we had followed the

Re: [Freesurfer] local gyrification index - contrast and doss vs. dods

On 02/21/2018 11:47 AM, C.P.E. Rollins wrote: > Dear Freesurfer Developers, > > I'm following the very well-documented steps proposed by Marie Schaer > for measuring local gyrification index in the paper "How to Measure > Cortical Folding from MR Images: a Step-by-Step Tutorial to Compute >

Re: [Freesurfer] Surface Errors

Hi Doug, They were initially reoriented for VBM analysis, but nothing else was changed (comparing original versus reoriented, there does not seem to be differences). The subjects are elderly (mean age = 74.08). We are investigating a new pre-dementia syndrome so there may be greater atrophy in

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

sorry Gabor, can you repost the rest of the thread? What was the artefact? On Mon, 26 Feb 2018, Gabor Perlaki wrote: > Does anybody else have a comment on the experienced artefact? > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] questions about the segamentation volume

Hi FreeSurfer Expert, I followed the Anatomical ROI analysis tutorial and make a aseg.vol.table for the 40 subjects. However, the segment volume can various a lot in different subjects, such as Left-Lateral-Ventricle, Left-Inf-Lat-Vent. I attached a screenshot. Thanks for your response. Best

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Does anybody else have a comment on the experienced artefact ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Does anybody else have a comment on the experienced artefact? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom

Re: [Freesurfer] Hippocampal Subfield Error

Dear Theo, Can you please provide us with the command you executed, and the complete output logs? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From:

Re: [Freesurfer] Surface Errors

Hi Emily, I looked over these subjects. While a few of the flagged spots are not really problems, most of them are true inaccuracies. I think the underlying problem is that your data is pretty noisy and have some ringing. What kind of acq was it? Scanner, field strength, pulse seq? Was it

[Freesurfer] aseg and aparcstats2table on longitudinal data

Hi FreeSurfer experts, I would like to use the asegstats2table and the aparcstats2table commands on my longitudinal data, that have been processing following the longitudinal pipeline (recon-all -cross, - base and finally -long). And I have two questions : 1) Am I obliged to do the

Re: [Freesurfer] thickness measure in basal ganglia

Hi Giovanni do you mean a cerebellar parcellation? We have several prototypes but haven't distributed anything yet. cheers Bruce On Mon, 26 Feb 2018, Giovanni de Marco wrote: Hello, is there an atlas for the cerebellum using freesurfer ? Many thanks for the information. Best Giovanni

Re: [Freesurfer] -make versus -all for edits

Hi Arkadiy -make all uses the makefile utility to only rerun the processing steps that are needed based on the timestamp of the various files in the subject's dir and a table of dependencies. cheers Bruce On Mon, 26 Feb 2018, Maksimovskiy, Arkadiy wrote: Dear Experts, I was wondering

[Freesurfer] -make versus -all for edits

Dear Experts, I was wondering if someone might be able to help me understand what the difference is between the two commands below. It seems that they can be used interchangeably, because I can forsee a situation in which one might not remember which command to run and also have done several

[Freesurfer] Hippocampal Subfield Error

Hi All, I tried to run a subject through FreeSurfer 6.0 for hippocampal Subfield segmentation but exited with errors. The content of the recon-all.error file is below. SUBJECT CHRM2001 DATE Sun Feb 25 00:34:13 GMT 2018 USER 15233963 HOST psych-sl03 PROCESSOR x86_64 OS Linux Linux

Re: [Freesurfer] thickness measure in basal ganglia

Hello, is there an atlas for the cerebellum using freesurfer ? Many thanks for the information. Best Giovanni 2018-01-11 9:15 GMT+01:00 de Marco : > Many thanks Bruce for your rapid and clear response. > Have a nice day > Best > Giovanni > > Envoyé de mon iPhone >