Re: [Freesurfer] visualizing paths stats by voxel

Hi Janosch - Are you by any chance using the dev version of freeview? a.y On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: Hi Anastasia and list, I'm trying to do analyses along the tract with the path_stats_byvoxel files. When I am visualizing the points using the waypoint functionality of

Re: [Freesurfer] [Tracula] pathstats.byvoxel.txt for between-group or correlational analyses

Hi Amelia - One day we'll have a proper statistical analysis function with multiple comparisons correction along the tract, but until then the name of the -stat option is mostly aspirational. It'll find the point-by-point correspondence among subjects and produce the table but you'll have to us

Re: [Freesurfer] TRACULA longitudinal processing fails when inter-subject registration to CVS template

Hi Daniel - You should be able to use CVS with longitudinal tracula, although it's probably the least tested combination of options in there. It sounds like this may be a bug. Can you please send me the full log file and full config file? Thanks! a.y On Tue, 4 Aug 2015, Daniel Myall wrote:

Re: [Freesurfer] Resending my questions: Issues with first attempt in viewing Tracula output

Hi Leora - I regret to inform you that it's the processing that has failed, pretty much for all the tracts. I'm guessing it's an earlier preprocessing (likely registration) step that has failed. If you upload the tracula output directories (dmri, dlabel, dpath) of your subject for me here, I

Re: [Freesurfer] Trac-all -stat

Hi Peggy - That's a good question and yet another great feature request. I can think of one completely inelegant hack for doing this right now in the absence of an actual feature. Let's say the path to the lh.cst stats of your subject is: subj1/blah...lh...blah/pathstats.byvoxel.txt

Re: [Freesurfer] tracula reinit failure filled my hard drive

Hi Peggy - It's trying out all the paths from all the atlas subjects for candidates to use to initialize the path in your subject. If it's having such a hard time finding a good candidate, I suspect that something went wrong earlier in the pre-processing, something like a serious registration

Re: [Freesurfer] Tracula - set echo spacing

Hi Celine - You can get this from the protocol print-out from the scanner. a.y On Mon, 13 Jul 2015, Celine Louapre wrote: > Hi Anastasia and Tracula experts, > We are running a new set of tracula analysis from Bay 6 and are > wondering how do we define the number of echo spacing in the dmrirc >

Re: [Freesurfer] mri_compute_volume_fractions with displacement map

No, there's not, sorry On 08/07/2015 03:48 PM, Sebastien Proulx wrote: > > Hello Freesurfer, > > I am trying to obtain csf, wm and gm tissue volume fraction maps that > matches my distorted high-resolution EPIs. > > Is it possible to input a displacement map to the > mri_compute_volume_fractions

[Freesurfer] mri_compute_volume_fractions with displacement map

Hello Freesurfer, I am trying to obtain csf, wm and gm tissue volume fraction maps that matches my distorted high-resolution EPIs. Is it possible to input a displacement map to the mri_compute_volume_fractions command, such that the surfaces will be deformed before computing the csf, wm and gm

Re: [Freesurfer] ID-swapping freesurfer data?

On 08/07/2015 03:11 PM, Nate Vack wrote: > Thanks. Any other file types I should look for tags in? I think the surfaces have the subject name imbedded in them. > > Out of curiosity, how do .mgz and nifti files differ? > mgz files have a lot more header info > Best, > -Nate > > On Thu, Aug 6, 2015

Re: [Freesurfer] ID-swapping freesurfer data?

Thanks. Any other file types I should look for tags in? Out of curiosity, how do .mgz and nifti files differ? Best, -Nate On Thu, Aug 6, 2015 at 9:28 AM Douglas N Greve wrote: > We don't have tools to explicitly change those strings. You can read > them into matlab as Bruce suggests. You can a

[Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag

Hi Freesurfer group, I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield of hippocampus. I followed the instruction written and was able to segment hippocampus subfields for number of MR images in one of the server. I followed the same instruction in another server w

Re: [Freesurfer] [FreeSurfer] 'unkown' voxels aprac+aseg.mgz

Dear Joseph, You can use the instructions on the following wiki pages for help with editing annotation files. The first one contains a tutorial on how to do this using tksurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit https://surfer.nmr.mgh.harvard.edu/fswiki/EditingLabels

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

yes, I wish we had the money to fund someone to do this, but alas it is very hard to get the NIH to fund such an effort On Fri, 7 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: FS has a lot of hidden capabilities that beginner users (like me) can find out by reading a proper documentation and sa

Re: [Freesurfer] mkanalysis-sess, timewindow

The psd window is only really relevant for FIR analyses. You are assuming a shape to the HRF (a gamma function), and so FSFAST hard codes the psdwin. If you really want to force it to change, put -timewindow after -gammafit On 8/6/15 4:38 PM, Xiaomin Yue wrot

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

FS has a lot of hidden capabilities that beginner users (like me) can find out by reading a proper documentation and save your time for more technical questions. Documentation doesn't correlate with how great FS and it's support community is. On Fri, Aug 7, 2015 at 11:11 AM, Bruce Fischl wrote:

[Freesurfer] flag -brainstem-structures is not working

Dear FS experts, I download the free surfer version 6.0.0 betha with the new functionality of automated segmentation of brainstem substructures for macOS. I already install matlabruntime, and follow all the steps required. But, when i tried to run the segmentation the following up error appears:

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

I guess only by looking at the code. We have tried to flesh out most of the documentation but have limited resources and person-power (and funding!) to do so. sorry Bruce On Fri, 7 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello Bruce, Is there any way to access the table of flag informa

Re: [Freesurfer] mri_deface

Hi Jurgen why not just use the defaced T1 as a mask for the DTI? Bruce On Fri, 7 Aug 2015, Jürgen Hänggi wrote: Dear FS experts I have to anonymize T1-w. and DTI images. I run mri_deface for T1-w. images successfully,  but I am wondering whether there is any easy way to also deface DTI imag

Re: [Freesurfer] Correction for multiple comparisons - qdec

You can try permutation, though it is often more constraining than those other two options. To do this, you'll need to run mri_glmfit-sim from the command line using the --sim perm option. Run it with --help to get examples On 8/7/15 6:59 AM, pablo najt wrote: Dear FS experts, I have a questi

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

Hello Bruce, Is there any way to access the table of flag information for mris_sphere? This page seems to e incomplete in that aspect. Many Thanks, Saeed On Fri, Aug 7, 2015 at 10:36 AM, Bruce Fischl wrote: > Hi Saeed > > we normally proj

Re: [Freesurfer] Fornix Segmentation

Hello again, FreeSurfer experts! I have another question for you...apologies if it seems rudimentary. Now that I've found the fornix segmentation file, I was wondering if it's possible to run mri_cc with the -f parameter in recon-all? I have already tried using an expert preferences file with mr

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

Hi Saeed we normally project onto the sphere, but if you want to generate a movie to show the idea you can give mris_sphere the flag -i, which will cause it to inflate to the sphere before unfolding. cheers Bruce On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Ok, but how about t

Re: [Freesurfer] mkanalysis-sess, timewindow

The psd window is only really relevant for FIR analyses. You are assuming a shape to the HRF (a gamma function), and so FSFAST hard codes the psdwin. If you really want to force it to change, put -timewindow after -gammafit On 8/6/15 4:38 PM, Xiaomin Yue wrote: The second number in the psdwin

Re: [Freesurfer] Label or Overlay of Surface files

Hi Lee, Perfect, Thanks. Saeed On Thu, Aug 6, 2015 at 5:15 PM, Lee Tirrell wrote: > Hi Saeed, > > You can run either of the following commands to overlay the ?h.sulc or > ?h.curv file: > > tksurfer subject hemisphere surface -snap -sulc > tksurfer subject hemisphere surface -snap -curv > >

Re: [Freesurfer] FSFAST

you can, but not from preproc-sess. This is controlled by mktemplate-sess which is called from preproc-sess, but you can run it separately. Specify the frame you want with -frame and run it with -force to force it to overwrite the other results. Then run preproc-sess (but not with -force !) and

Re: [Freesurfer] mri_deface

Hi Jürgen, Personally, I don't think defacing is necessary for most DTI data. Assuming your slices don't cover the face (which most DTI data doesn't include), I think you are safe to say the data is inherently defaced. Others may have other ideas. hth d On 8/7/15 6:53 AM, Jürgen Hänggi wrote:

[Freesurfer] mri_deface

Dear FS experts I have to anonymize T1-w. and DTI images. I run mri_deface for T1-w. images successfully, but I am wondering whether there is any easy way to also deface DTI images with mri_deface or whether someone has already defaced DTI images with another tool. Thanks in advance Best regards