Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1 {Disarmed}

External Email - Use Caution Hello Ali, I would try using the RPM installer which should at least check some dependencies on X packages, system libraries, etc.,  https://secure-web.cisco.com/1QZVOusYuqG6pzgftW11woMO3J7wlOTz6CpOKDAkTB2PSKdv7HWkk1N4ZgDbrS9Ofxy-S0PLYnkCeiBbxFw3i6PW1_

[Freesurfer] Freesurfer 7.1.0 on CentOS 8.1

External Email - Use Caution Hello, I’ve seen a couple mentions on the list-serv about difficulties using Freesurfer on CentOS 8. My issue is likely similar, but I have a few more details. I downloaded freesurfer-linux-centos8_x86_64-7.1.0.tar.gz. When I launch `freeview`,

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed}

External Email - Use Caution I tried following codes according to the suggestions, the terminal reported an error: cannot do frame average without input volume mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.areapial.label (Thi

Re: [Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed}

External Email - Use Caution Dear Douglas, Thank you very much for your rapid response. I have another question. I am following the FS Repeated Measures tutorial and therefore, I ran this: mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh --fsgd rm

Re: [Freesurfer] Welcome to the "Freesurfer" mailing list {Disarmed}

External Email - Use Caution Hello Nicholas, Please check you setting for the environment variable FREESURFER_HOME.  I used the Mac 7.1.1 release package from https://secure-web.cisco.com/1UkHJYwewl8qS85O_CWV-J5WUiafp7vGnbHtJ7jYex3q0G5kU2j5BECwnS7n9fZB3i0kvic0yZqcpw3vXMEiw3il7sAI

[Freesurfer] [FreeSurfer] Two Postdoctoral Fellowships in Aging and Alzheimer's disease {Disarmed}

External Email - Use Caution We are seeking two highly motivated postdoctoral researchers to lead NIH-funded projects in the Laboratory for Cognitive and Translational Neuroscience directed by Dr. Hwamee Oh at Brown University. One position is to use fMRI and PET to study visual me

Re: [Freesurfer] mri_glmfit_sim error (Douglas N. Greve)

External Email - Use Caution Hi Douglas, This is for a lGI analysis. I used a fwhm of 10 and not 38: mri_surf2surf --hemi lh --s fsaverage --sval lh.lgi.mgh --fwhm 10 --cortex --tval lh.lgi.10B.mgh So why am I getting this error? cannot find > /usr/local/freesurfer/average/mul

Re: [Freesurfer] Different Sequences Longitudinal Stream {Disarmed}

Hi Lee It's really hard to say. The change in voxel size might sound trivial, but it is a 30% change in volume (and hence SNR). The longer TE will counteract that by increasing T2* weighting. Sorry I don't have anything more conclusive to say except that it is obviously not ideal Bruce From: f

[Freesurfer] Different Sequences Longitudinal Stream {Disarmed}

External Email - Use Caution Dear FreeSurfer experts, I am currently working on a longitudinal data set with 4 time points, acquired at one site with the same Siemens Trio 3T scanner. Unfourtunately, the T1 sequence differs slightly for one of these time points. These sequences

Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC {Disarmed}

External Email - Use Caution The subcortical structures were not delineated correctly, especially the nucleus caudatus which had a lot of atrophy in this particular patient group. Kind regards Donatienne Op do 5 nov. 2020 om 15:50 schreef Douglas N. Greve : > I don't think CAT c

Re: [Freesurfer] mris_anatomical_stats error: stating file

Hi, Yes, sorry! I copied the error message from terminal, but copied the command from my script so I copied the error message for the wrong hemisphere. I apologise for the confusion. I've attached the terminal output (I've put # at the lines above the error message) and the script I use in

Re: [Freesurfer] trac-preproc error

Hi Anastasia, I uploaded the files. Let me know if you have trouble viewing them! Best, Yasemin From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia Sent: Monday, November 2, 2020 10:57 PM To: Freesurfer support list Subject: Re: [Free

Re: [Freesurfer] LGI quality control {Disarmed}

When you click on the gray areas, is the value 0 or just something very close to 0? You may need to set the lower threshold (default is 2). Also, I would recommend using freeview via tksurferfv (same command line as tksurfer) On 11/4/2020 2:12 PM, Nelson, Eric wrote: External Email -

Re: [Freesurfer] .mgh file unknown, GLM paired analysis {Disarmed}

External Email - Use Caution Dear FS experts, I have removed the backslashes "\" and now it works, so problem solved. Thank you very much. Regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psyc

Re: [Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed}

In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer your question, the first example you give is the right way to handle it. On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote: External Email - Use Caution Dear Freesurfer experts, I am trying to do a longitudinal

Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC

I don't think CAT creates white or pial surfaces, so no. What is wrong with your FS analysis? On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote: External Email - Use Caution Dear, The segmentation using Freesurfer was incorrect, however we have a good segmentation from Cat 12. Ca

Re: [Freesurfer] (no subject)

Try this instead aparcstats2table --hemi lh  --subjects subj10 --parc aparc.a2009s  --meas meancurv --tablefile /home/team33/ aparcstats.txt On 11/3/2020 12:20 PM, saman fouladi wrote: External Email - Use Caution hi I run in linux command: ""

Re: [Freesurfer] mris_anatomical_stats error: stating file

Is that the right error msg? It says it can't find the RH, but you are running it with LH. Can you post the entire terminal output? On 11/3/2020 2:00 PM, Chan, Shi Yu wrote: Hi FreeSurferDevelopers, I'm trying to calculate cortical thickness statistics from the Yeo 17 Network cortical pa

Re: [Freesurfer] Fixing error with pial surface {Disarmed}

Try these instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log  into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a pa

Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all {Disarmed}

Hi Andy, this is a bug introduced in 7.1.1, some kind of race condition. You can fix it by commenting out this line in recon-all   if($OMP_NUM_THREADS > 1 && ! $LHonly && ! $RHonly) set cmd = ($cmd --parallel) # just hemis doug On 11/3/2020 12:06 PM, Andy Worth wrote: External Email

Re: [Freesurfer] Question about smoothing for extracting anatomical stats {Disarmed}

This is not needed or recommended. Not needed because you are already averaging over space and not recommended because it would cause one region to bleed over into another. On 11/3/2020 7:00 AM, Hye Min Shin wrote: External Email - Use Caution Hello experts, So I understand that whe

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed}

Try --slabel fsaverage lh /path/to/lh.areapial.label On 11/2/2020 10:24 PM, 李梦君 wrote: External Email - Use Caution Thank you very much! I tried to extract the areas with the following codes: mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel lh.areap

Re: [Freesurfer] mri_convert error

It looks like it is trying to extract diffusion info. Try running it with --no-dwi On 11/2/2020 5:11 PM, Georgina Angelopoulou wrote: External Email - Use Caution Dear Freesurfer Developers, I am sorry I did not include the error message. I am attempting to convert some dicom files t

Re: [Freesurfer] mri_glmfit_sim error

Information about multiple comparisons correction has been pre-computed for various parameters, including the FWHM. In this case, the measured FWHM (38) is outside of the precomputed range. 38 is extremely high. Is this a thickness study? What smoothing level did you apply (--fwhm in mri_glmf

[Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed}

External Email - Use Caution Dear Freesurfer experts, I am trying to do a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment). Although I have run a paired t-test, now I would like to do a repeated measu

[Freesurfer] Join the Brainhack donostia

External Email - Use Caution The Basque Center on Cognition, Brain and Language (BCBL) is holding a free online next week. We hope that it can be of interest to this community, and that you could forward others this information. At the BCBL, we are organizing the third edition o

[Freesurfer] aparcstats2table

External Email - Use Caution hi I run in linux command: """ aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj10/stats --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats .txt """