Re: [Freesurfer] macOS Sierra installation error

Hi Narae Try running bash first Cheers Bruce > On May 14, 2018, at 10:57 PM, NR K wrote: > > Narae ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] macOS Sierra installation error

External Email - Use Caution Hello FreeSurfer Developers, My name is Narae. I'm attempting to install Freesurfer on MacOS Sierra 10.12.6. I already followed step-by-step manual on the freesurfer wiki. I installed XQuartz 10.11 and complete the installing process. But there

Re: [Freesurfer] Contrast interpretation - between-groups mean

External Email - Use Caution Many thanks, Doug! Should I then rely on groups' means to determine the 'direction of the result', and not on the 'max statistical significance' signal? Does 'abs' simulation sum up the results I could get by running 'pos' and 'neg' simulations

[Freesurfer] pcc.nii.gz vs z.nii.gz resting state

External Email - Use Caution Dear freesurfers, I’m using mri_glmfit to estimate the correlation between a time series from a seed region and all the voxels in the brain. For one subject I get values in the pcc.nii.gz around .4 in my region of interest (not seed) but the z-scores

Re: [Freesurfer] Contrast interpretation - between-groups mean

You have specified "abs" meaning an unsigned "absolute" test, so there is no guarantee that the mean contrast will be pos or neg. On 05/14/2018 06:11 PM, Pedro Rosa wrote: > > > Here it is: mri_glmfit-sim --glmdir > PEP-HC_Gender_Age.txt.lh.area.mgh.5.mgh.cortex.glmdir --sim-sign abs >

Re: [Freesurfer] Contrast interpretation - between-groups mean

External Email - Use Caution Here it is: mri_glmfit-sim --glmdir PEP-HC_Gender_Age.txt.lh.area.mgh.5.mgh.cortex.glmdir --sim-sign abs --cache 1.3 abs On Mon, May 14, 2018 at 6:59 PM, Douglas N. Greve wrote: > sorry, one more thing. Can you send your

Re: [Freesurfer] Contrast interpretation - between-groups mean

sorry, one more thing. Can you send your mri_glmfit-sim command line? On 05/14/2018 05:46 PM, Pedro Rosa wrote: > > > Hi, Doug. Many thanks. > Find the fsgd and the contrast attached, as well as the cluster > summary and the individual-based cluster data (which I used to > calculate the

Re: [Freesurfer] Contrast interpretation - between-groups mean

External Email - Use Caution Hi, Doug. Many thanks. Find the fsgd and the contrast attached, as well as the cluster summary and the individual-based cluster data (which I used to calculate the groups' means). The cluster I referred to is the second one (medialorbitofrontal). I

[Freesurfer] Reminder to Register for HCP Course 2018

External Email - Use Caution Only a few weeks until the *2018 HCP Course: "Exploring the Human Connectome"*! For more info and to register visit the HCP Course 2018 website . A limited number of

Re: [Freesurfer] volume to surface registration

Thanks for the reply! Zhuonan 发件人: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Douglas N. Greve [dgr...@mgh.harvard.edu] 发送时间: 2018年5月14日 15:02 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] volume to

Re: [Freesurfer] Contrast interpretation - between-groups mean

Can you send your fsgd file and contrasts? On 05/14/2018 01:25 PM, Pedro Rosa wrote: > > > Dear FreeSurfers, > I got results from a cortical area analysis that intrigued me: Upon > the inspection of clusters that survived Monte-Carlo simulation, I > found a cluster with larger area among a

Re: [Freesurfer] Extract time-courses by ROI from preproc-sess preprocessed data

You can map the fmri volume into the anatomical space, something like mri_vo2vol --mov fmri.nii --reg register.dof6.lta --fstarg --o fmri.anat.nii.gz (Note fmri.anat.nii.gz will be a big file that you may not want to keep around) Then run mri_segstats, like mri_segstats --i fmri.anat.nii.gz

Re: [Freesurfer] ASEG Extraction Inquiry

On 05/10/2018 02:44 PM, David S Lee wrote: > > > Hi FreeSurfer Experts, > > I have extracted ASEG volumes using "asegstats2table" and have a few > questions about the output. > > 1. I get values of "0" for Left and Right "WM-hypointensities" as well > as "non-WM-hypointensities". Does the ASEG

Re: [Freesurfer] volume to surface registration

Probably best to run recon-all on the mni152, then sample your 152 data onto the surface, then use the surface-based registration. On 05/10/2018 01:06 PM, Wang, Zhuonan wrote: > Hi Team, > > I have a functional image which located in the FSL volume-based > template(MNI152), and now I wanna to

Re: [Freesurfer] FS_Fast preproc-sess - bbregister misalignment

External Email - Use Caution OK - the 5.3 or the 6.0 version? 2018-05-14 20:00 GMT+02:00 Douglas N. Greve : > Can you tar up one of your subjects (fmri and FS analysis) and send it > to me on our file drop below? > > > On 05/14/2018 01:58 PM, Patrycja

Re: [Freesurfer] FS_Fast preproc-sess - bbregister misalignment

Can you tar up one of your subjects (fmri and FS analysis) and send it to me on our file drop below? On 05/14/2018 01:58 PM, Patrycja Naumczyk wrote: > > > Hi Doug, > > we have v.6.0 on a cluster, so I quickly run one subject there (the > one, whose files and pictures I attached previously).

Re: [Freesurfer] FS_Fast preproc-sess - bbregister misalignment

External Email - Use Caution Hi Doug, we have v.6.0 on a cluster, so I quickly run one subject there (the one, whose files and pictures I attached previously). This time the BBR-sum was 0.9476, so slightly better but still bad :( Best regards, Patrycja 2018-05-14 16:56

[Freesurfer] Contrast interpretation - between-groups mean

External Email - Use Caution Dear FreeSurfers, I got results from a cortical area analysis that intrigued me: Upon the inspection of clusters that survived Monte-Carlo simulation, I found a cluster with larger area among a first group in contrast to a second group. However, when I

Re: [Freesurfer] FS_Fast preproc-sess - bbregister misalignment

It might be the initialization with FLIRT. Do you have access to FS6.0? If so, can you try running 6.0 instead to see if it fixes the problem? On 5/14/18 4:05 AM, Patrycja Naumczyk wrote: Hi All, I'm still struggling with the registration - so far I tried performing slice-timing and/or

Re: [Freesurfer] differences between qdec display and summary file for monte carlo corrected results

qdec should not be used for correction of multiple comparisons. Use mri_glmfit-sim directly instead. On 5/11/18 10:32 PM, yuanchao.zha...@gmail.com wrote: Hi, freesurfer experts, As I mentioned in my last email, I see no answer. I think it is possible that my description is not clear

Re: [Freesurfer] mris_preproc error

You probably need to regenerate this file: /autofs/space/alicudi_002/users/mscat/users/gabriel/R01_Automatic/MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/overlay/lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh On 5/11/18 2:39 PM, Barletta, Valeria wrote: > Hi Freesurfers, > I used

[Freesurfer] Postdoc position at Bangor University, UK

External Email - Use Caution Applications are invited for a two year (with a possible 1-2 year extension), full time postdoctoral position with Dr. Kami Koldewyn in the Developmental Social Vision lab in the School of Psychology

Re: [Freesurfer] FS_Fast preproc-sess - bbregister misalignment

External Email - Use Caution Hi All, a little update. I tried running fslreorient2std before preprroc-sess. It didn't help either... Best regards, Patrycja pon., 14.05.2018, 10:05 użytkownik Patrycja Naumczyk < patrycja.naumc...@gmail.com> napisał: > Hi All, > > I'm still