Re: [Freesurfer] Inquiry about process time by use "recon-all"

Hi Bruce, Thanks for your suggestion, the “-openmp” flag can shorten process time over 70%. Ritthikrai. On 13/1/18 03:29, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: Hi

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Dear Iglesias, Do you think that it is useful to also use a fieldmap for hippocampal subfield segmentation? Can Freesurfer's hippocampal subfield segmentation use it? I'm not sure that due to the limited resolution of the fieldmap and due to registration issues it is worth to acquire a fieldmap

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

Wonderful...and makes total sense! Thankyou...it is off and running now. -Dianne On Mon, Jan 22, 2018 at 8:19 PM, Chris Gorgolewski < krzysztof.gorgolew...@gmail.com> wrote: > Hi Dianne, > > You need to "mount" the using -v the same way input and output directories > are mounted. For example:

[Freesurfer] freesurfer bids app cannot find license file

After trying the example bids app (which worked fine), I am trying the freesurfer bids app: https://github.com/BIDS-Apps/freesurfer I have built the docker container on my mac and I have the ds005 data directory here and the license.txt which I requested from freesurfer. I asked for a linux

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

Hi Dianne, You need to "mount" the using -v the same way input and output directories are mounted. For example: docker run -ti --rm -v /Volumes/Main/Working/BIDS_ TESTING/license.txt:/license.txt:ro -v /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v

Re: [Freesurfer] TRACULA QC

Hi Linnea – Before the stats are computed, the probability distribution of the paths is thresholded to 20% of its peak value, so voxels with very low probability will not affect the outcome. Best, a.y From:

Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

Hi Carissa – You mentioned that your DWIs had 2mm isotropic resolution, but the data that I received is 1x1x2mm, so it has a larger matrix size. Is there any chance that some form of preprocessing was done that resulted in upsampled data, or was it acquired this way? Best, a.y From:

Re: [Freesurfer] FreeSurfer Installation

try this page: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#FreeSurferDownloadandInstall cheers Bruce On Mon, 22 Jan 2018, Caio Quini wrote: > Hello > > I am trying to download FreeSurfer from freesurfer.net and I can't open the > download page. > It keeps returning an error

[Freesurfer] FreeSurfer Installation

Hello I am trying to download FreeSurfer from freesurfer.net and I can't open the download page. It keeps returning an error message. Is that a common error? Is there any other way to download the software? Thank you very much. Regards Caio Quini

Re: [Freesurfer] Which Dev Version is Best?

Oh! Okay thanks for pointing this out. I’m rebuilding a fixed distribution right now - I’ll let you know when the link’s been updated. thanks Andrew On January 22, 2018 at 2:50:13 PM, Maksimovskiy, Arkadiy (amaksimovs...@mclean.harvard.edu) wrote: Hi

Re: [Freesurfer] Which Dev Version is Best?

Hi Andrew, Thank you so much for the info. and for the quick response. For some reason when I tried that version, I got an error when opening Freeview (error: Qt platform plugin "cocoa" missing). I reinstalled the older Dev version which did not give me these issues. I would like to upgrade

Re: [Freesurfer] Which Dev Version is Best?

Hi Arkadiy, You should use the OSX-ElCapitan dev version, it’s the most up-to-date and contains new patches. We’ve recently upgraded the mac dev builds from OS X Lion (10.7) to El Capitan (10.11), so you’re in the clear if you’re using Sierra (10.12). This is a relatively recent change, so let

Re: [Freesurfer] Anatomical ROI analysis

Hi Ting, this is a bug introduced by python3, you must run this script with python2 by either modifying the first line to say: #!/usr/bin/env python2 or by running: python2 $FREESURFER_HOME/bin/asegstats2table --subjects 004 021 040 067 080 092 --segno 11 17 18 --tablefile aseg.vol.table best,

[Freesurfer] Which Dev Version is Best?

Dear Experts, I was wondering if the OSX-ElCapitan Dev version of freesurfer is only for ElCapital? It has a later date of modification than the “dev” version, so I wanted to check, in case it has new patches. I am running OSX-Sierra, and would love to hear which one would be best. Thank you,

Re: [Freesurfer] recon-all error

Hi Julia it sounds like we aren't able to read this flavor of dicom properly (since it seems like we think it's a diffusion scan). Are you sure you have the right series? If so, maybe try converting it to nifti then giving the nifti volume as input to recon-all? cheers Bruce On Mon, 22 Jan

Re: [Freesurfer] Hippocampal subfields segmentation

Hi Alexis, Yes please send me the images! Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Alexis Guyot

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, I think I’ve discovered the source of this issue. It’s tough to troubleshoot it without access to the subject set, but I think I have a working fix. The patch link (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface) is updated with the new

[Freesurfer] Hippocampal subfields segmentation

Dear Freesurfer developers, I have been trying to segment (with Freesurfer v6.0.0, on Ubuntu 14.04) the hippocampal subfields of two 7T MR images in NIFTI format: an isotropic (0.8*0.8*0.8 mm3) whole-brain T1-weighted source volume with an anisotropic (0.3*1.2*0.3 mm3) T2-weighted volume covering

Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline

If your fwhm is 0, then something is wrong. Look in the fwhm.dat file in the glmfit output to see what the value is. Also, send the terminal output from mri_glmfit (not mri_glmfit-sim) On 01/22/2018 11:43 AM, miracle ozzoude wrote: > > -- Forwarded message -- > From: *miracle

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

The problem is that the surfreg command is failing. Thanks, Lanbo On Thu, Jan 18, 2018 at 5:14 PM, Douglas Greve wrote: > Is the problem that the surfreg command is failing or that you don't know > how to apply LME? > > On 1/17/18 9:55 AM, lanbo Wang wrote: > > Hi

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

that's good to hear, thanks for letting us know Michelle Bruce On Mon, 22 Jan 2018, Michelle VanTieghem wrote: Hi,  I went ahead and re-processed all of our data with the newest version (6.0) of freesurfer (I didn't hear back from anyone on this issue for over a month). It does make a

[Freesurfer] Fwd: monte-carlo error in longitudinal pipeline

-- Forwarded message -- From: miracle ozzoude Date: Sat, Jan 20, 2018 at 1:56 PM Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline To: Freesurfer support list Hello Doug, I tried using the MC tables that

Re: [Freesurfer] Linear Mixed Effect Modle

Hi, I used 5.3 version. And it worked after I deleted empty line. And it works when I use 6.0 version. Thanks for your help! Best, Lanbo On Mon, Jan 22, 2018 at 10:16 AM, Diers, Kersten /DZNE < kersten.di...@dzne.de> wrote: > Hi, > > do you happen to use Freesurfer version 5.3 or maybe

Re: [Freesurfer] Linear Mixed Effect Modle

Hi, do you happen to use Freesurfer version 5.3 or maybe earlier? It seems to me that in the 5.3 version empty lines in the qdec-long file (sub_long.dat in your case) were not skipped by the mris_preproc script, hence the 'nsubjects = 80' message although there are only 79 "subjects"

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

oh, then I think you are just showing the surface-based label, which will only fill voxels that intersect with the white surface I believe. To sample it into the volume try mri_label2vol with the --fill-ribbon flag (the help is pretty extensive). cheers Bruce On Mon, 22 Jan 2018,

Re: [Freesurfer] convert nii to nii.gz

Dear Bruce, Thanks for your response. I will check it today. Best, Ting > On Jan 21, 2018, at 10:41 AM, Bruce Fischl wrote: > > Hi Ting > > if you can't see the share folder then you can't access our binaries. Maybe > talk to your local sysadmins? > > cheers >

Re: [Freesurfer] recon-all error

Hi Julia, I’m sure one of the Freesurfer experts will reply soon. Perhaps this will be helpful though. It looks like recon-all is failing to find you dicom images. You might want to post the recon-all command sequence you are using for them. The first thing to check is that you are providing

[Freesurfer] recon-all error

Dear FreeSurfer developers,   I am new to FreeSurfer and this is the first time I am working with MR images.   I’ve been trying to run recon-all for my first subject and I keep getting errors like:   ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File:

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Dear Bruce, Thank you for your answer! I just display the "T1.mgz" image (mri folder) using Freeview and then loaded the "lh/rh.perirhinal_exvivo.label" rois (label folder). If this is not the good way to do it, please, could you explain more the procedure? What do you mean by MT and PC?

Re: [Freesurfer] Hippocampus Subfield analysis error

Hi Hannah, This seems like a more general problem with your PATH, but I’m sure Andrew (CCed) has a better idea of what might be going on. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com