Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Hi, I've also come across similar situations in my FS 6.0 dataset. I have tried tweaking the seg-wlo and seg-ghi values and these steps have led to marked improvements in some cases. Curious to hear from the FS team too. Thanks. Best Wishes, Elijah Elijah Mak, Research Associate Depar

[Freesurfer] White matter atrophy

Dear Freesurfer experts, I know how to do cortical thickness group analysis using Freesurfer, also I know how to use Qdec to compare groups regarding gray matter volume differences, cortical thickness, curvatures, area,... etc. I am wondering if there is any way in Freesurfer to study the differe

Re: [Freesurfer] Any advices for hires surface reconstruction?

Hi, Thank you for your reply Douglas, I will talk with my supervisor about an eventual contribution. Best, Damien Douglas Greve Tue, 18 Apr 2017 18:41:59 -0700

[Freesurfer] Need help to run freesurfer

Dear Experts, I have installed in /usr/local/freesurfer. I am trying to follow the command given in the freesurfer web page. $> export FREESURFER_HOME=/usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh But I could not figure out the .sh file in the freesurfer folder. Please see

[Freesurfer] help mri_surf2vol

Hi, Is there a way to have the destrieux parcellation on a volume format ? .nii for example. I tried to used mri_surf2vol without success for now: mri_surf2vol --subject 0001GRE_25-11-2014 --merge /home/b67-belledone/freesurfer/subjects/0001GRE_25-11-2014/mri/T1.mgz --so /home/b67-belledone/frees

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Agreed. A validated protocol run on a very large group of subjects in 5.3 was attempted with similar data in 6.0 and not only was the longitudinal edit stream nearly non-functional for white matter edits, cross edit performance was disappointing. I am currently waiting on a response to these po

Re: [Freesurfer] Need help to run freesurfer

I just did a test by downloading and extracting the tar, and I got all the expected files: /usr/local/fstemp/freesurfer/tkmeditParcColorsCMA /usr/local/fstemp/freesurfer/mni /usr/local/fstemp/freesurfer/sources.csh /usr/local/fstemp/freesurfer/docs /usr/local/fstemp/freesurfer/Simple_surface_labe

Re: [Freesurfer] White matter atrophy

Hi John - Unless someone else has a better idea, the aseg (subcortical segmentation) contains left and right cerebral and cerebellar white matter labels. You can look at the ROI analysis tutorial for how to extract stats from aseg labels. Best, a.y From: freesu

Re: [Freesurfer] mri_glmfit error with aparc table flag

Hello Doug, I downloaded and installed octave. However, I can't find the annotval2surfoverlay.m file in the matlab directory of freesurfer. Does it come with FS v6 or do i need to download the file? Also, I was looking into the annotval2surfoverlay file and I have couple of questions. % Run these c

Re: [Freesurfer] White matter atrophy

Thank you a.y, I am sorry if my question was not clear enough! In Qdec/ tab "design" the user have the choice to choose the analyses that he wants to conduct on aseg,mgz, wmparc.mgz or aparc+aseg.mgz. These atlases report white and gray matter volumes. in Qdec, if I choose volume from the dropdow

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Hi Antonin if you upload this subject and give me the voxel coords of that location I'll take a look cheers Bruce On Wed, 19 Apr 2017, Antonin Skoch wrote: > Dear experts, > > I am sending just one more example to illustrate issue with white surface > estimation in v6.0. See the attached scree

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Thank you for looking into the deeper mechanics of this issue. In my case I am dealing with motion contaminated 1.5T data which require extensive and somewhat intricate edits to the white matter bleed into the pial surface, as well as into dura. In working with a past dataset of similar characte

Re: [Freesurfer] mri_glmfit error with aparc table flag

you can get it here https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m On 04/20/2017 10:10 AM, miracle ozzoude wrote: > Hello Doug, > I downloaded and installed octave. However, I can't find the > annotval2surfoverlay.m file in the matlab directory of freesurfer. > Does it

Re: [Freesurfer] help mri_surf2vol

Hi Pierre use, you can try mri_aparc2aseg. cheers Bruce On Thu, 20 Apr 2017, pierre deman-kibleur wrote: > > Hi, > > Is there a way to have the destrieux parcellation on a volume format ? .nii > for example. > I tried to used mri_surf2vol without success for now: > > mri_surf2vol --subject 0

Re: [Freesurfer] R: Re: R: Re: FSGD file FS-FAST

On 04/19/2017 04:37 PM, std...@virgilio.it wrote: > I'm sorry but it not clear to me. There are 2 factors, 2 levels, while I have > 1 > Factor, 4 Levels It is still four groups. > In particular, have I looked to difference between Group1+Group2 vs > Group3+Group4? > Is it correct 0.5 -0.5 0.5 -0

Re: [Freesurfer] volume in native space of .vtk file in mni152 space

You can use mri_segstats passing newoutputfile as the --seg On 04/19/2017 06:47 PM, Corinna Bauer wrote: > Dear all, > > I have a series of .vtk files in MNI152 1mm space from an external > thalamus atlas outlining specific thalamic nuclei. I would like to put > these into native subject space

Re: [Freesurfer] Using registration.dat to register a dataset

I don't know what you are trying to do. Can you elaborate? On 04/19/2017 07:26 PM, Jacobson, Aaron wrote: > Hello, > > I am new to freesurfer. I have been looking for an answer to this > issue for days. > > I ran bbregister to align a dti scan to a t1 struc. > > It worked beautifully. > > I am t

Re: [Freesurfer] mri_glmfit error with aparc table flag

Thank very much Doug. Also, I was looking into the annotval2surfoverlay file and I have couple of questions. % Run these commands in matlab % annotnames = strvcat('superiortemporal','insula','postcentral'); % annotvals = [1.1 2.2 3.7]; % annotfile = '~/paul_analysis/fsaverage/label/lh.aparc.annot'

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Hi Antonin yes, the -mprage flag is likely to be at least one source of the differences. It makes the normalization more aggressive (since mprage trades higher CNR for lower SNR). I'm surprised removing it didn't help. I think that changing things like wlo could also help depending on how wron

Re: [Freesurfer] White matter atrophy

Not other than just comparing the total WM volume. I guess you could do some type of VBM analysis, but I would recommend using a package that specializes in that type of analysis On 04/20/2017 07:42 AM, John Anderson wrote: > Dear Freesurfer experts, > I know how to do cortical thickness group

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Hi David I can take a look at a subject of yours as well if you upload it (both 5.3 and 6.0 processed versions if you have them) and point me at voxel coords. The white surface is by design insensitive to local variations which is what makes it robust, but also makes it more difficult to modif

Re: [Freesurfer] mri_glmfit error with aparc table flag

On 04/20/2017 11:08 AM, miracle ozzoude wrote: > Thank very much Doug. Also, I was looking into the > annotval2surfoverlay file and I have couple of questions. > % Run these commands in matlab > % annotnames = strvcat('superiortemporal','insula','postcentral'); > % annotvals = [1.1 2.2 3.7]; >

Re: [Freesurfer] plot-twf-sess display error

display is an imagemagick program. It is used to display the images created by gnuplot. If you have xv installed, you can add -xv to the command line. Otherwise, install imagemagick https://www.imagemagick.org/script/index.php On 04/19/2017 04:03 PM, Xie, Wenting wrote: > Hi all, > > > I am

Re: [Freesurfer] Using registration.dat to register a dataset

Absolutely, thanks for looking into this. I have 3 datasets: 1. T1 anatomical 2. DTI 3. Unusual dataset (derived from DTI) that does not have a contrast that bbregister can use to register the data I want to register the unusual dataset (#3) to the T1 anatomical. Since the unusual dataset can

Re: [Freesurfer] Using registration.dat to register a dataset

Yes, when using mri_vol2vol or mri_vol2surf, spec the unusual data set as the --mov but pass the bbregister registration to the --reg flag. On 04/20/2017 11:41 AM, Jacobson, Aaron wrote: > Absolutely, thanks for looking into this. > > I have 3 datasets: > > 1. T1 anatomical > 2. DTI > 3. Unusual

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Dear Bruce, I am uploading 3 example subjects processed both by v5.3 and v6.0 I referred to in the screenshots in my previous posts: Subj 1 - large leak of white surface outside brain in v6.0, not present in v5.3. RAS coords -53,-1,75 Subj 2 - another measurement of identical subject - white su

Re: [Freesurfer] Using registration.dat to register a dataset

Thanks a lot! That worked well! The registration is not perfect, but it is much better than the original. I used the command: mri_vol2vol --mov PathTo/UnusualData.nii.gz --targ PathTo/orig.nii.gz --interp nearest --o PathTo/UnusualData_toT1reg.nii.gz --reg PathTo/dti2t1.dat Is there anything

Re: [Freesurfer] Using registration.dat to register a dataset

That command looks right. If the unusual volume was derived in a voxel-for-voxel way from the DTI, then its registration should be just as good On 04/20/2017 12:11 PM, Jacobson, Aaron wrote: > Thanks a lot! That worked well! The registration is not perfect, but it is > much better than the ori

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Thanks Bruce I’ll prepare something and upload it, hopefully before the weekend. I’ll let you know when I’ve got it uploaded. Best, David P. Semanek, HCISPP Research Technician, Posner Lab Division of Child and Adolescent Psychiatry Columbia University Medical Center New York State Psychiatric I

Re: [Freesurfer] White matter atrophy

On 04/20/2017 10:21 AM, John Anderson wrote: > Thank you a.y, > I am sorry if my question was not clear enough! > In Qdec/ tab "design" the user have the choice to choose the analyses > that he wants to conduct on aseg,mgz, wmparc.mgz or aparc+aseg.mgz. > These atlases report white and gray matt

[Freesurfer] R: Re: R: Re: R: Re: FSGD file FS-FAST

I would look for differences among 4 different groups (A, B, C, D). e.g. I expected that the impaiment is AMessaggio originale >Da: "Douglas N Greve" >Data: 20-apr-2017 17.07 >A: >Ogg: Re: [Freesurfer] R: Re: R: Re: FSGD file FS-FAST > > > >On 04/19/2017 04:37 PM, std...@virgilio.it wrote

[Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

Hi FS Experts, I’m having trouble getting anatomical stats from a parcellation I made out of scanner-space volume ROIs. I have taken the following steps to do this. mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o myROI_orig.nii.gz --interp nearest mris_sample_parc Subj111 lh myR

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Hi Antonin Doug points out to me that you edited your copy of recon-all in 5.3, which makes it really hard for me to track down any differences. For sure your recon-all used cubic interpolation for conforming by default, which introduces pretty big differences right at the start that I expect

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Dear Bruce, sorry for the confusion with xopts-use and recon-all editing. I have checked the xopts-use and the reason of this is that I run the subject 1 and 2 as a part of batch job on large amount of subjects, where I rerun recon-all to anonymize them. Some of them had expert-options file

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Hi Antonin it is a pretty significant difference, even visually, and it occurs right at the start of everything, so the differences propagate forward through recon-all. I only looked at subject 1, but it is a case where the intensities are ambiguous between gray and white and a slight increase