[Freesurfer] dimension mismatch longitudinal

External Email - Use Caution Hello Freesurfers! In regards to the link below: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36839.html Is there a way to fix a dimension mismatch? Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.__

Re: [Freesurfer] Problems with freesurfer 7.1.0

External Email - Use Caution Thank you! > Il giorno 28 mag 2020, alle ore 20:27, Hoopes, Andrew > ha scritto: > > Hi Angela, > > This is a bug on osx, which does not have the --preserve=timestamps flag > available to cp. This will be fixed in the next 7.1 patch, but in the

Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

Hi Marina can you upload this subject? I'm not sure what is going on. Or send us the recon-all.log? The vertex error means that the surfaces don't match. This usually means that you recreated some but not all of the surfaces for one of the hemis cheers Bruce On Thu, 28 May 2020, Marina

Re: [Freesurfer] fs_install_mcr error

Hi Amir, Is there any other terminal output? My guess is that the installer did not download correctly in the temporary directory. Best Andrew From: on behalf of AmirHussein Abdolalizadeh Reply-To: FS Help Date: Wednesday, May 27, 2020 at 12:02 PM To: FS Help Subject: [Freesurfer] fs_insta

Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

You can use ANTS N3 by adding -ants-n3 to the command line. In theory, you can use a mask, but I vaguely remember that there was a bug when someone tried it in our code On 5/28/2020 12:37 PM, Schranzer René wrote: External Email - Use Caution Hi Douglas, Thanks for your help! Two

Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

External Email - Use Caution Hi Bruce, The talairach transform is reasonable and the aseg segment the cc correctly. I run with freesurfer dev version the same command (recon all -autorecon-2wm -subjid post_006) and now I have more information about what could be the problem. The

Re: [Freesurfer] Problems with freesurfer 7.1.0

Hi Angela, This is a bug on osx, which does not have the --preserve=timestamps flag available to cp. This will be fixed in the next 7.1 patch, but in the meantime, you can fix this manually via: cd $FREESURFER_HOME/bin sudo rm rca-long-tp-init sudo curl https://raw.githubusercontent.com/freesu

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

External Email - Use Caution Is it the pctsurfcon tool? ( https://surfer.nmr.mgh.harvard.edu/fswiki/pctsurfcon) On Thu, May 28, 2020 at 10:12 AM Bruce Fischl wrote: > External Email > > David and Doug: can you point Prad in the right direction for looking at > gray and white sig

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

External Email - Use Caution Hi Dr. Fischl, Thank you for suggesting that. Would it be possible to share a link to a page with information about this stream or to a patch? Thanks, Prad On Thu, May 28, 2020 at 9:46 AM Bruce Fischl wrote: > External Email > > I see. I think Doug

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

David and Doug: can you point Prad in the right direction for looking at gray and white signal changes and ratios? On Thu, 28 May 2020, Pradyumna Bharadwaj wrote: External Email - Use Caution Hi Dr. Fischl, Thank you for suggesting that.  Would it be possible to share a link

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

I see. I think Doug has a more modern stream for this that David Salat has also used a lot On Thu, 28 May 2020, Pradyumna Bharadwaj wrote: External Email - Use Caution Hi Dr. Fischl, Thanks for confirming that! We were broadly interested in testing whether age-related differen

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

External Email - Use Caution Hi Dr. Fischl, Thanks for confirming that! We were broadly interested in testing whether age-related differences in cortical measures were impacted by the CNR in each ROI. Best, Prad On Thu, May 28, 2020 at 9:33 AM Bruce Fischl wrote: > External Em

Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

External Email - Use Caution Hi Douglas, Thanks for your help! Two more questions: Is it possible to use the individual brain mask of my skull stripped data as a "mask image" for the step of the NU Intensity correction in recon-all with an additional flag to carry out a better b

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

Hi Prad what is your goal? What you describe below should work cheers Bruce On Thu, 28 May 2020, Pradyumna Bharadwaj wrote: External Email - Use Caution Hi Dr. Fischl, Thank you for clarifying that! As a follow up question, I just wanted to double check that the method out

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

External Email - Use Caution Hi Dr. Fischl, Thank you for clarifying that! As a follow up question, I just wanted to double check that the method outlined in this post is still a valid approach to obtaining the CNR values for each of the ROIs in the Desikan-Killiany atlas ( https

Re: [Freesurfer] mri_cnr label flag

Hi Prad if you use the cortex.label is will avoid using the non-cortical regions in the surface, like the midline, so should be a more accurate measure cheers Bruce On Thu, 28 May 2020, Pradyumna Bharadwaj wrote: External Email - Use Caution Hi, I had a question about th

[Freesurfer] mri_cnr label flag

External Email - Use Caution Hi, I had a question about the -label flag in mri_cnr. 1) When you do not use the -label option and just use the following command: mri_cnr $FREESURFER_HOME/subjects/bert/surf $FREESURFER_HOME/subjects/bert/mri/norm.mgz The output is as follows w

Re: [Freesurfer] AAL parcellation for Freesurfer

Not that I know of. I played around a little with them. Below are my notes on getting it onto the colin27 brain. Good luck! Downloaded AAL from http://www.gin.cnrs.fr/spip.php?article217, specifically http://www.gin.cnrs.fr/AAL/aal_for_SPM8.tar.gz The ROIs are in ROI_MNI_V4.nii, but they need t

Re: [Freesurfer] lta_convert

lta_convert was not introduced until 6.0. You can just copy it from 6.0 into 5.3 On 5/28/2020 11:24 AM, Alshelh, Zeynab wrote: Hi everyone, I am running this version of fs: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 But I am having trouble running lta_convert, it returns with command

Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

You can use it with all subjects then On 5/28/2020 3:28 AM, Schranzer René wrote: External Email - Use Caution All subjects. Best, René *Von:*freesurfer-boun...@nmr.mgh.harvard.edu *Im Auftrag von *Douglas N. Greve *Gesendet:* Mittwoch, 27. Mai 2020 18:37 *An:* freesurfer@nmr.mgh

[Freesurfer] lta_convert

Hi everyone, I am running this version of fs: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 But I am having trouble running lta_convert, it returns with command not found. Is there something I am missing? Thanks Zeynab Alshelh, PhD | Postdoctoral Research Fellow Pain and Neuroinfla

Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

have you also looked at the talairach transform to make sure it is reasonable? And does the aseg segment the cc properly? That is, does it label it as wm as it crosses from one hemi to the other? On Thu, 28 May 2020, Marina Fernández wrote: External Email - Use Caution Hi Br

[Freesurfer] AAL parcellation for Freesurfer

External Email - Use Caution Dear all, does anyone know if there is a surface parcellation file based on the AAL for freesurfer? I am aware that I could recon-all the MNI brain and project the atlas on the surface. (but maybe someone already did that) I spend some time googeling

Re: [Freesurfer] FS6: Mapping data to fsaverage6

External Email - Use Caution Nevermind, I solved it. One has to replace '--s subject1' with '--s fsaverage6' in the call to mri_surf2surf. Makes sense. The lh.fsaverage6.sphere.reg file is not needed. Tim > On May 28, 2020 at 11:00 AM Tim Schäfer wrote: > > > Externa

Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)

Hi Elizabeth, segment_T1.sh uses a bunch of files in native space for initialization that you’d also have to deform, if you wanted to run it in MNI space. I think the easiest would be to run it in native space, and then warp the segmentation to MNI, using e.g., the registration given by CVS. Chee

[Freesurfer] Postdoctoral position on real-time layer-fMRI at 7T available at MPI in Leipzig

External Email - Use Caution Postdoctoral position on real-time layer-fMRI at 7T The Max Planck Institute for Human Cognitive and Brain Sciences (MPI CBS) in Leipzig (Germany) invites applications for a Postdoctoral Researcher Positionin the Department of Neurophysics with Dr. R

[Freesurfer] Postdoc position available - computational modeling and real-time fMRI neurofeedback of language

External Email - Use Caution With the launch of a new ‘NCCR Evolving Language’ (http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglanguage_en.pdf), which involves nearly 40 different research groups from a large variety of disciplines across Switzerland, we

Re: [Freesurfer] FS6: Mapping data to fsaverage6

External Email - Use Caution Hi Doug, thanks for your answer, that worked: mris_apply_reg --src subject1/surf/rh.thickness --streg subject1/surf/rh.sphere.reg fsaverage6/surf/rh.sphere.reg --trg subject1/rh.thickness.fsaverage6.mgz I do now want to smooth the data. For an FWHM

Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

External Email - Use Caution Hi Bruce, Yes, everything seems normal in the input files of mri_fill. We review it slice by slice in freeview. Do you know what could have happened? Best regards, Marina

Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

External Email - Use Caution All subjects. Best, René Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Douglas N. Greve Gesendet: Mittwoch, 27. Mai 2020 18:37 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.