Re: [Freesurfer] Building from source #3 -- dynamic binding

Hello Yaroslav, I believe there is already an option that can be set at configure time to build dynamical;ly, though I have not tried it. e.g., maybe it causes the libraries that Freesurfer builds internally to be built as shared instead of static. However, at least in out nightly builds, the fr

[Freesurfer] Freesurfer and crypt

I have a couple of users here who are reporting that on machines with FIPS enabled, which in turn disables certain cryptographic functions, FreeSurfer core dumps with a call to the crypt() function, which FIPS disables. Someone speculated based on output from strace that this is FreeSurfer possibl

[Freesurfer] Building from source #3 -- dynamic binding

Dear FreeSurfer developers, I would like to pick up on this elderly theme by wondering: Would you be philosophically opposed against patches/pull requests which introduce dynamic linking for freesurfer build? Would anyone from the FreeSurfer team be interested to pursue such an effort? The id

[Freesurfer] which dev version for amygdala segmentation

Hi All, How do I download reqd. files / FS developmental version to run hippocampal/amygdala pipeline as described in the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala I tried downloading the el capitan version of the development version of freesurfer fro

Re: [Freesurfer] Hemodynamic Lag Shift

Thanks, Doug. I added (-4s) delay and plotted the data but I got the same delay as no shift. Also I did (+4) delay and lost most of the activation. Do you have any recommendations? Thanks, Sarah On Wed, Mar 28, 2018 at 4:39 PM, Douglas N. Greve wrote: > You can use the -delay flag in mkanalys

[Freesurfer] Longitudinal data from different sequences and scanners

All, Our lab is working with longitudinal (two time points) data from a cohort of around 130 individuals. We are attempting to make comparisons between time points 1 and 2 on measures like total brain volume, ventricular volume, ventricle-brain-ratio, and cortical thickness. However, we have run

[Freesurfer] mirroring fsaverage labels between hemispheres

Hi, I have pored over (I think) all of the mailing list postings about cross-hemisphere mapping and I can't quite figure out how to do this. I have a bunch of labels on fsaverage, and I want to be able to check/visualize the relationship between lh and rh versions of the labels. I can do mri_labe

Re: [Freesurfer] defining input images in a for-loop in recon-all

yes, that would work cheers Bruce On Thu, 29 Mar 2018, Darko Komnenić wrote: Hi Bruce, thanks for the reply. I only have one acquisition per subject. I guess I can make a separate text file with a list of paths to dicoms and then somehow try to pair the path and the subject name in the recon-al

Re: [Freesurfer] defining input images in a for-loop in recon-all

Hi Bruce, thanks for the reply. I only have one acquisition per subject. I guess I can make a separate text file with a list of paths to dicoms and then somehow try to pair the path and the subject name in the recon-all command. > From: Bruce Fischl > Subject: Re: [Freesurfer] defining input ima

[Freesurfer] A new member to freesurfer mailing list

Hi FreeSurfer experts , I am Xiao Yang, who is a visiting research fellow in McLean Hospital, Harvard Medical School. I am writing to ask to be added to the FreeSurfer mailing list. Here is my email address: yangxiaokx...@gmail.com Thank you so much! Best wishes, Xiao Sent from Mail for Wi

Re: [Freesurfer] Information on FS-FAST

yes, you have to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz, then when you run fcseed-config, specify -seg yourseg.mgz -segid yoursegid On 03/29/2018 05:36 AM, Piero Chiacchiaretta wrote: > > Thanks Doug. > > My goaI is to perform a FC analysis of cerebe

Re: [Freesurfer] convert labels to volume in MNI?

By using -reg $FREESURFER_HOME/average/mni152.register.dat you are indicating that the input label is in fsaverage space. You need to have a registration from your source space (VPNL) to the MNI152. If you have a whole brain in VPNL, then you can run recon-all on it to generate surfaces. Do the

Re: [Freesurfer] defining input images in a for-loop in recon-all

Hi Darko sorry, you need to sort this out yourself as there is no way for us to know where the dicoms are. An alternative is to create each subject dir, create the 00?.mgz files (if you have more than one acquistion) in the /mri/orig dir, then run recon-all without the -i flag. If you use -i

Re: [Freesurfer] Information on FS-FAST

Thanks Doug. My goaI is to perform a FC analysis of cerebellum subregions using FS-FAST. I understand that FS do not permit the segmentazion for 601-602. Anyway, do you think that I can use as seed the cerebellar regions defined by Buckner et al.(http://www.freesurfer.net/fswiki/CerebellumParcel

[Freesurfer] "preproc-sess" with intermediate volume

Dear all, I have a problem with the command: "preproc-sess" I wanted to use the Registration option to add an intermediate volume. The only documentation I could find about it was the one that appears with the command: "preproc-sess --help" Registration options -init-fsl : use fsl to initial

[Freesurfer] defining input images in a for-loop in recon-all

Dear experts, I would like to run a for-loop in FreeSurfer 5.1. so that I can have multiple subjects analyzed over the holiday, without having to come to the lab and start each of them myself. I searched the previous emails in this list and know that I can make a file with a subject list, and then