[Freesurfer] Retinotopy, design ill-conditioned

External Email - Use Caution Hello experts, I'm performing retinotopy analysis but when running the command selxavg3-sess It starts, but after some lines, I get the following error: ERROR: design is ill-conditioned I don't know how to proceed from here to solve the erro

[Freesurfer] recon-all in freesurfer

External Email - Use Caution Dear all,I'm working on brain surface with conformal geometry algorithms, I need to know whether triangular mesh that gets from "recon-all" in Freesurfer is a Delaunay triangular mesh !? Very thanks in advance 

Re: [Freesurfer] recon-all in freesurfer

no, sorry, it is not cheers Bruce On Thu, 2 Jan 2020, Fatemeh Ahmadi wrote: External Email - Use Caution Dear all, I'm working on brain surface with conformal geometry algorithms, I need to know whether triangular mesh that gets from "recon-all" in Freesurfer is a Delaunay tria

Re: [Freesurfer] Problem for mri_glmfit

the ICV has a very different scale than the rest of the variables. Try subracting the mean and dividing by the stddev to bring it within range of the other variablse On 12/24/2019 12:58 PM, Gwang-Won Kim wrote: External Email - Use Caution Dear Sir, I ran "mri_glmfit" commend. I had n

Re: [Freesurfer] vol2subfield

Copy it to $FREESURFER_HOME/bin (or anywhere in your path) Make sure to make it executable with chmod a+x vol2subfield On 12/30/2019 6:57 PM, std...@virgilio.it wrote: External Em

Re: [Freesurfer] FSFAST registration

On 12/30/2019 7:55 PM, Star Xi wrote: External Email - Use Caution Dear FS experts, I’m processing the task-related fMRI using FS-FAST. I check the quality assurance and modified some subjects’ registration file(named new one as “register_manual.lta”). Then I do the first level analy

Re: [Freesurfer] mkanalysis-sess.new not found

Use mkanlaysis-sess. Why are you trying to use the .new version? On 12/31/2019 5:45 AM, Marco Ninghetto wrote: External Email - Use Caution Dear experts, my name is Marco and I'm using freesurfer to perform retinotopy analysis and I am having a problem with command: `mkanalysis-ses

Re: [Freesurfer] highres fMRI selxavg error

Why are you combining them into one bold folder? On 12/30/2019 9:09 AM, Nasiriavanaki, Zahra wrote: Dear Freesurfer experts Happy Holidays! I have a subject with two highres fMRI scan sessions. Attached you can see an image, showing how I organized the sub-folders. I preprocessed the bold1 and b

Re: [Freesurfer] Obtaining pre&post values from longitudinal dataset without cross-base-long

Yes, that will work On 12/21/2019 11:45 AM, Tudor Popescu wrote: External Email - Use Caution Dear FS experts, From a pre-&post-intervention data set, is it possible to extract thickness values at those two time points just by using recon-all, that is, without running the full longitu

Re: [Freesurfer] matlab output issue

It says that there is only one time point in that data. Are you sure that run is fMRI? Try mri_info 007/f.nii.gz and see how many time points it has On 12/20/2019 8:56 AM, Baptista, Paulo wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm helping researchers test Fre

Re: [Freesurfer] mapping the reliability of separating GM/WM

The surf/?h.w-g.pct.mgh is a map of the white-gray percent difference On 12/20/2019 9:13 AM, Bruce Fischl wrote: sure, you should be able to make vertex-wise maps. I think Doug wrote something to do this, but if not I can modify mri_cnr to output mean and variance maps for gray and white easily

Re: [Freesurfer] Fill holes in BOLD surface

how did you creaet this? On 12/20/2019 10:10 AM, Marina Fernández wrote: External Email - Use Caution Hi Freesurfer experts, I have projected 4D-preprocessed BOLD data to Freesurfer cortical surfaces. Resulting individual surfaces have many holes (see attached image) that I would like

Re: [Freesurfer] Unable to run recon all

Can you send the recon-all.log file? You sent the .error file On 12/20/2019 10:13 AM, Sahil Bajaj wrote: External Email - Use Caution Hello FS experts, I am trying to run recon all on about 100 subjects. But one out of 100 subjects finishes recon all with error, and doesn't complete th

Re: [Freesurfer] (no subject)

Can you send me the subject data following these steps? 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

Re: [Freesurfer] highres fMRI selxavg error

I need to concatenate the two sessions. We scanned the subjects twice with the same task. I need to see the maps for each session separately and also together. Thanks Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital

Re: [Freesurfer] mkanalysis-sess.new not found

External Email - Use Caution Thank you for your reply. I tried with mkanalysis-sess but something went wrong. I think I posted the problem in this web list as well. My retinotopy stimuli take 200seconds to make an entire run (one cycle) and we use TR = 2.5 sec. From what I saw in

Re: [Freesurfer] highres fMRI selxavg error

When you say you need to see them together, what does that mean? Are you computing contrasts between the two sessions or you just want to combine them statistically? On 1/2/2020 10:07 AM, Nasiriavanaki, Zahra wrote: I need to concatenate the two sessions. We scanned the subjects twice with the

Re: [Freesurfer] highres fMRI selxavg error

I want to concatenate the two sessions which I guess is the same as combining them statistically. Please note that it's all done in "self" space not fsaverage. Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13

[Freesurfer] Changelog between stable and dev versions?

External Email - Use Caution Hello everyone, and happy new year. I know it's never a good idea to mix versions within a study, but that's what has happened in a large study here, so I am trying to get a sense of what changes there have been. I was wondering if there is a way to se

[Freesurfer] Different versions of fsaverage?

External Email - Use Caution Are the fsaverage versions coming from the following (as reported in recon-all.log within the fsaverage directory) significantly different ? freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20101225 freesurfer-x86_64-redhat-linux-gnu-dev4-20090216 freesur

Re: [Freesurfer] Changelog between stable and dev versions?

You can probably get a list of the changes from github, but there is no way to separate out which ones are major and which ones are minor. On 1/2/2020 11:36 AM, Dorian P. wrote: External Email - Use Caution Hello everyone, and happy new year. I know it's never a good idea to mix version

Re: [Freesurfer] Different versions of fsaverage?

Probably not. The main diff between the current dev and stable 6 is that stable 6 had some big triangles near the top of the head On 1/2/2020 11:39 AM, Dorian P. wrote: External Email - Use Caution Are the fsaverage versions coming from the following (as reported in recon-all.log withi

Re: [Freesurfer] highres fMRI selxavg error

The easiest thing to do is to probably do the concatenation by hand, eg, mri_concat subj/sess01/analysis/contrast/ces.nii.gz subj/sess01/analysis/contrast/ces.nii.gz --o ces.sess01+sess02.nii.gz mri_concat subj/sess01/analysis/contrast/cesvar.nii.gz subj/sess01/analysis/contrast/cesvar.nii.gz --o

[Freesurfer] Surface file format differences

External Email - Use Caution Hello, When working with the nightly development version of FreeSurfer recon-all (freesurfer-linux-centos6_x86_64-dev.tar.gz 23-Dec-2019 06:01) The surface file format differed by one character (\n) from previous versions. What makes me suspicious of t

Re: [Freesurfer] tracula error gradient vectors too many ('s

Hi Andrade - You have some forward slashes ("/") at the ends of lines in the config file that should be backslashes ("\") instead. a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Renew Andrade Sent: Saturday, December 21, 2019 9:11 AM To: Freesur

Re: [Freesurfer] highres fMRI selxavg error

Thanks a lot for your reply. I have one more question about selxavg error and I appreciate if you could reply. I have another subject which has been scanned in 7T. When I run selxavg, it doesn't go through for the left and right hemi, but it gets perfectly done for subcortex. I attached the lo

Re: [Freesurfer] highres fMRI selxavg error

It appears to be dying on this command mris_fwhm --mask /autofs/space/oprah_001/users/zn025/fearcond_7T/all_subjects/ylug_ass_sess01/bold/cond.lh/mask.nii Can you run it from the shell and send the terminal output? On 1/2/2020 2:13 PM, Nasiriavanaki, Zahra wrote: Thanks a lot for your reply. I

Re: [Freesurfer] highres fMRI selxavg error

I did run it from the shell and figured out what the problem was! Thanks a lot!! Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129 __

Re: [Freesurfer] (no subject)

External Email - Use Caution Dear Douglas, I uploaded two files: 1122.tar.gz is the sample subject and BN_Atlas_freesurfer.tar.gz this is the Atlas I want use for the cortical and subcortical parcellation/segmentation. Thank you so much, Boris > Am 02.01.2020 um 17:06 schrieb

[Freesurfer] Run Recon-all Parallel on Linux

External Email - Use Caution Dear Freesurfer experts, May I know how to run Recon-all in parallel on Linux? I have read some source said that can use "gnu parallel" to complete it. But they do not describe it in detail how to perform it. Regards Frank -