[Freesurfer] Freesurfer V6 installation: ubuntu virtual machine

External Email - Use Caution Dear Freesurfer experts, Just a simple question, is possible to install the Freesurfer (Version 6) in a virtual machine of ubuntu? Thanks in advance, Best regards, Steve ___ Freesurfer mailing list

[Freesurfer] Hippocampal subfields: exporting results

External Email - Use Caution Dear Freesurfer experts, I used the freesurfer dev version to estimate hippocampal subfields using mode B (additional scan). All have worked fine although when I tried to export the results I can not find the txt file created This is the output

Re: [Freesurfer] Hippocampal subfields: exporting results

External Email - Use Caution Dear Eugenio, I noticed what was the problem. I used freesurfer dev version with the following command: segmentHA_T2.sh I tried to export the hippocampal and amygdala results of several subjects with these commands and now everything works fine.

[Freesurfer] T2 in recon-all: command to correct pial surfaces errors

External Email - Use Caution Dear Freesurfer experts, I used t2 image as input in subjects that have already been processed without them following the instructions of the website. Although pial surface segmentation has improved there is still some error. After edit the

[Freesurfer] Local Gyrification Index: freesurfer version

External Email - Use Caution Dear Freesurfer experts, What freesurfer version do you recommend to perform the local gyrification index, version 6 or 6 development version? Thanks in advance. Best regards, ___ Freesurfer mailing list

[Freesurfer] Freesurfer dev version: Hyppocampus, amygdala and thalamus segementation

External Email - Use Caution Dear Freesurfer devs, We are considering segmenting with the Freesurfer 6 dev version the hippocampus, the amygdala and the thalamus of several subjects who have already done the recon-all. Since we have a T1 image and T2 image with smaller voxel

[Freesurfer] Volume correction with Intracranial volume

External Email - Use Caution Dear Freesurfer experts, I would like to perform external analysis with the hippocampus, parahipocampus and entorhinal volume. As I understand its the hipocampo volume should be corrected using the subject´s intracranial volume. 1. How do you

[Freesurfer] Correlation between Hippocampal subfields - behavioural test

External Email - Use Caution Dear Freesurfer experts, I would like to perform a correlation between the volume of subiculum and some behavioural measures. Before making that correlation, is it necessary to correct the subiculum volume with the eTIV? I have thought of doing it by

Re: [Freesurfer] Correlation between Hippocampal subfields - behavioural test

bic_volume before perform the regression using the folliwng formula: subic_vol = average_eTIV_allsample * subic_vol / eTIV_subject Thank you. Best, Steve. El mié., 22 abr. 2020 a las 17:35, Steve Petersen () escribió: > Dear Freesurfer experts, > > I would like to perform a correlation

[Freesurfer] Results summary in QDEC

External Email - Use Caution Dear Freesurfer experts, I performed group analysis in QDEC in order to compare cortical thickness between two groups using the Monte Carlo Z simulation correction. My question is, where is located the z-score of each significant cluster? Maybe in the

[Freesurfer] Hippocampal subfields questions

External Email - Use Caution Dear Eugenio, Just two simple questions about hippocampal subfields: Q1. The volume of each hippocampal subfield is exported in mm3? Q2. I would like to compare hippocampal subfields volume measures between three groups by including the eTIV as

[Freesurfer] Correlation between thickness and csf_measures: vector

External Email - Use Caution Dear Freesurfer experts, I am conducting a cortical thickness study in three groups. After performing the between-group analyses, I would like to evaluate the possible correlation between cortical thickness and the levels of some csf measures. To do

[Freesurfer] Group Analysis: Comparing four groups

External Email - Use Caution Dear Freesurfer experts, This is the first time I perform group analysis in Freesurfer. My aim is to compare the cortical thickness in four groups matched in age, sex and years of education using the Monte Carlo multiple comparisons correction. I

[Freesurfer] C.Thickness: Statistical analyses with three groups

External Email - Use Caution Dear Freesurfer experts, My goal is to compare the cortical thickness between three groups. For that purpose, I performed whole brain analysis with a F-contrast to evaluate a group effect. Since the F-test was significant, I performed pairwise

[Freesurfer] SAMSEG for Alzheimer´s Disease study

External Email - Use Caution Dear Freesurfer experts, We are working with a large MRI dataset (FLAIR, T1) of healthy adults and adults with mild cognitive impairment. Can we use SAMSEG to segment white matter lesions in this population?. Thanks for your help! Best, Steve.

Re: [Freesurfer] Cohen´s D effect size

c 2021 a las 19:14, Steve Petersen () escribió: > Dear Freesurfer experts, > > I am attempting to estimate the Cohen's D effect size of significant > clusters using the suggested command > <https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix3

[Freesurfer] Freesurfer: Re-run recon-all in older versions

External Email - Use Caution Dear all, We conducted the recon-all and applied a quality control protocol in several subjects using the FSurfer 6 version. Now, we would like to run the recon-all again on an older version of FSurfer (5.3 v) but considering the edits we made on

[Freesurfer] Cohen´s D effect size

External Email - Use Caution Dear Freesurfer experts, I am attempting to estimate the Cohen's D effect size of significant clusters using the suggested command

[Freesurfer] FSGD file and constrast

External Email - Use Caution Dear FreeSurfer experts, I have MRI data of one group of subjects and would like to evaluate positive and negative correlations between cortical thickness and some biomarkers by excluding the potential effects of age and sex. I followed the FS

[Freesurfer] Autorecon-pial with T1w and T2w images

External Email - Use Caution Dear FreeSurfer experts, After reviewing and manually editing the recon-all outputs in freeview, I'm going to re-run the recon-all command with the autorecon-pial flag. My question is, does the autorecon-pial also take into account the T2w image or

[Freesurfer] Recon-all in post stroke aphasic patients.

External Email - Use Caution Dear FreeSurfer experts, I would like to run the recon-all command in MRI images of post-stroke aphasic patients. Should I use a particular flag in the recon-all command to avoid important errors during cortical reconstruction?. We are only interested

[Freesurfer] T1w/T2w ratio maps: acquisition parameters T1w and T2w

External Email - Use Caution Dear FreeSurfer experts, I would like to calculate myelin maps using the ratio between T1w and T2w scans. However, the acquisition parameters of the T2w images are slightly different (e.g.* voxel size T1w* = 1mm3* vs* *voxel size T2w* = 0.35 mm3 ;*