Re: [Freesurfer] Error using selexavg3-sess

Just following up on this - thanks! > On Sep 29, 2015, at 1:29 PM, Morenikeji Adebayo > wrote: > > Hi there, > > I’m running into difficulty executing the “selexavg3-sess” command for a few > participants. For example, when I run the command: > > foreach c(lh rh mni305) > selxavg3-sess -anal

[Freesurfer] Fwd: Re: PVE correction tool within the V 6 beta

Forwarded Message Subject:Re: [Freesurfer] PVE correction tool within the V 6 beta Date: Thu, 1 Oct 2015 17:08:07 +0200 (CEST) From: m.ba...@ulg.ac.be To: Freesurfer support list Dear Greve, Thank you for your answer. Steps 1 and 2 are ok but in step 3 the

Re: [Freesurfer] warping surface label to volume space

Hi Doug, Thanks for checking the data! I just removed the output volume, ran the command again and got the same weird output. Since it worked for you, I tried it again… no change. However, then I noticed that the mri_vol2label uses the SUBJECTS_DIR path and this was not set to this folder (I was t

Re: [Freesurfer] mris_surf2vol

not really - that's the price you pay for voxelizing. I guess you could thicken it a bit or fill the ribbon and do some type of morphological erosion On Fri, 2 Oct 2015, Kevin Aquino wrote: Ah sorry for not being clear, Basically I would like the output from mris_surf2vol with the mask option

Re: [Freesurfer] fsaverage error with recon-all

Try removing -ba_labels (it will do that with -all anyway) On 9/29/15 9:02 PM, 葉丁瑞 wrote: Dear All, I ran the following script: recon-all -i /Volumes/yang/S002_AD1118_20090116/NCKU-0003--1.dcm -s S002_ba -sd /Volumes/yang/S002_AD1118_20090116/ -all -ba_labels and got the error below at

Re: [Freesurfer] warping surface label to volume space

I'm at a loss here. I run the exact same command with the same version. I get the same terminal output, but my output volume looks ok. The only thing I can think of is that there is an old version that output volume that is not getting overwritten. Can you name the output file differently and m

Re: [Freesurfer] Error Messages for Accessing Bin

Hi, Thank you very much for your response. The output of that command was: tle7@sni-vcs-gotlib:~$ ls -l /home/tle7/freesurfer/bin/mri_convert -rwxrwx--x 1 tle7 stanford 1672136 Aug 15 2010 /home/tle7/freesurfer/bin/mri_convert tle7@sni-vcs-gotlib:~$ On Fri, Oct 2, 2015 at 10:39 AM, dgw wrote:

Re: [Freesurfer] mri_convert doubles file size when changing TR header information

It is probably changing the data type from short to float. Try adding -odt short --no_scale 1 You can also look at the data type with mri_info --type file.nii On 10/1/15 10:52 AM, Shaun Patel wrote: > I noticed after running slice-time correction with SPM, the resulting Nifti > files do not

Re: [Freesurfer] ] dt_recon

I don't think I would use "DTI Morphometry" to describe it. I'm not sure what term I would use. It is basically a FA ROI analysis On 10/2/15 1:28 PM, Alshikho, Mohamad J. wrote: Hi Doug, Thank you very much for your answers! Kindly I have one more question: At the end of DTI analysis using the

Re: [Freesurfer] Group Analysis

What you use depends on what you are trying to do. Starting with the sig.mgh is good because it has not been corrected for multiple comparisons. You have a pretty high threshold (4, which means p<.0001). Try lowering it to 2 or even 1.3 to see if any activation pops out. At some point you'll ne

Re: [Freesurfer] Group Analysis

Sorry, as I am quite new to this type of analysis, does the sig.mgh show any significance? if so how can I report it? I mean are they saved somewhere in SUBJECTS_DIR? Also, it seems the corrected one does not show anything, am I true? The last thing about this, shall I use sig.mgh or F.mgh? Many

Re: [Freesurfer] Error Messages for Accessing Bin

Timothy, What is the output of this command: ls -l /home/tle7/freesurfer/bin/mri_convert ? hth d On Fri, Oct 2, 2015 at 1:36 PM, Timothy Quang-Tin Le wrote: > Hi, > I tried the chmod command, but it did not work. How I check that I've > downloaded the correct version? > Thank you very much >

[Freesurfer] Error Messages for Accessing Bin

Hi, I tried the chmod command, but it did not work. How I check that I've downloaded the correct version? Thank you very much Timothy On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl wrote: > can you try chmod a+x on one of them and see if it can then be executed? > e.g.: > > chmod a+x /home/tle7/f

[Freesurfer] ] dt_recon

Hi Doug, Thank you very much for your answers! Kindly I have one more question: At the end of DTI analysis using the tool “dt_recon” we will have “ stats” file including the FA value for every segment and parcellate in the brain. Depending on this output can we use the term “ DTI morphometry” t

Re: [Freesurfer] mris_surf2vol

Try using Method 1 from this version of mri_surf2vol ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol On 10/2/15 11:38 AM, Kevin Aquino wrote: Ah sorry for not being clear, Basically I would like the output from mris_surf2vol with the mask option to be less speckled

Re: [Freesurfer] Group Analysis

what about them? On 10/2/15 1:20 PM, Ali Radaideh wrote: Thanks Douglas, The second line worked fine, but can I show you the results attached to this email? Thanks, Ali On Fri, Oct 2, 2015 at 7:22 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: I notice from the image t

Re: [Freesurfer] Parcellation stats

Try cd $SUBJECTS_DIR/subject/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.yeo.stats -b -a ../label/lh.yeo2011_17Networks_N1000.annot -c ../label/aparc.annot.ctab subject lh white On 10/2/15 12:19 PM, Ali Radaideh wrote: I am trying to extract the cort

Re: [Freesurfer] Group Analysis

I notice from the image that the overlay is turned off. Try turning it on. Also, you can try tksurferfv fsaverage lh inflated -aparc -ov sig.mgh If that does not work, then tksurfer fsaverage lh inflated -aparc -ov sig.mgh On 10/2/15 12:08 PM, Ali Radaideh wrote: Hi, I am running a group a

Re: [Freesurfer] Parcellation stats

I am trying to extract the cortical volume, thickness, and area based on these 17Networks cortical parcellation. Thanks, Ali On Fri, Oct 2, 2015 at 6:23 PM, Douglas Greve wrote: > You should not use both --seg and --annot. What are you trying to > accomplish? > > On 10/2/15 3:34 AM, Ali Radaide

Re: [Freesurfer] mris_surf2vol

Ah sorry for not being clear, Basically I would like the output from mris_surf2vol with the mask option to be less speckled. For example, in the image attached: http://www.physics.usyd.edu.au/~aquino/example_mri_surf2vol.png there are some voxels missing. Is there an option to fill these voxels?

Re: [Freesurfer] FreeSurfer Ubuntu Server

Your best bet I fear might be to try and build FreeSurfer yourself on your specific distro of Ubuntu. https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS While not impossible (we have done this), it does require some detailed knowledge of Linux in general and Ubuntu in particular as you

Re: [Freesurfer] Parcellation stats

You should not use both --seg and --annot. What are you trying to accomplish? On 10/2/15 3:34 AM, Ali Radaideh wrote: Hi Bruce, I have used the following command line: mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum and got the

Re: [Freesurfer] FreeSurfer Ubuntu Server

Thanks for you reply, Rudolph. We have a cluster environment in our university, and the best Ubuntu version to us for now is Ubuntu 12.04 (in a closest future we will update to a newer version, but not now...). In the download page there is only FreeSurfer for CentOS, Mac and a Virtual Machine of

Re: [Freesurfer] mris_surf2vol

Hi Kevin I'm not clear on what you need. Would mri_surf2vol --fillribbon do what you want? I don't really know what else "voxelize" means cheers Bruce On Fri, 2 Oct 2015, Kevin Aquino wrote: Hi all, I am trying to "voxelize" the cortical surfaces generated in freesurfer and I am a little st

Re: [Freesurfer] White Matter Edits vs. Control Points, & third party software

Hi Alberto 1. No, this is not the same. The control points are used to estimate the bias field, which can affect an entire regions. Replacing a voxel in the brainmask with a 110 will only affect that voxel. 2. You can do this if you want but you have to be careful how you edit. When we turn

Re: [Freesurfer] White matter Error

Hi Trinh can you just attach the images? Your link didn't work for me. You can check the topology of the surface computationally using mris_euler_number. You might also try moving backwards/forwards a few slices to try to understand what is going on. cheers Bruce On Fri, 2 Oct 2015, Thục T

[Freesurfer] Statistical tests on Tracula's path spline

Hi, Thanks for the great FreeSurfer Course this past week. After running through Tracula and extracted the path stats (by voxel) across all subjects, can I apply mri_glmfit to test the group differences using the generated txt file that has all subject's diffusion meassure (e.g., FA) along part

[Freesurfer] mris_surf2vol

Hi all, I am trying to "voxelize" the cortical surfaces generated in freesurfer and I am a little stuck. I have been using mris_surf2vol with the --mask option however this generates a very speckled representation of the cortical surface on the voxels. What I would prefer would be the level sets

Re: [Freesurfer] White Matter Edits vs. Control Points, & third party software

Alberto, I included detailed replies below, but I have a question before you get to those. Why don't you want to follow the FreeSurfer techniques for reconstruction? You suggested several other ways, but I don't understand your motivation for not wanting to follow the instructions for FreeSurfe

[Freesurfer] Cannot change min threshold in Configure Overlay Display TKSurfer

Dear developers/users? When I load a *mgh.sig* file in *TkSurfer* and I go on *Configure Overlay Display* and want to change the *min Threshold on 1.3* or wathever number I can't edit or do that? did somebody encounter the same problem? How can you solve it? Thank You. -- Oana Georgiana Rus

Re: [Freesurfer] Hippocampus visualisation

That's super Eugenio, Thanks so much. Exactly what I needed. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu] Sent: 02 October 2015 10:57 To: Freesurfer support list Subject: Re: [Freesurf

Re: [Freesurfer] Hippocampus visualisation

Hi Erik, one possible way of doing this: 1. For a single subfield: set the color map to Lookup Table. Tick "show as isosurface in 3d view". Tick "label volume". Then, set both values of the range to the numeric code of the subfield you want to display (e.g., for CA1, it would be 206). 2. For

[Freesurfer] White Matter Edits vs. Control Points, & third party software

I have some questions about how to manually correct the white matter regions . It's the same manually edit the volume "brainmask.mgz" and use control points? Would I get the same result? My intention is not to use control points, but directly replace the voxels that have not been classified as whi

[Freesurfer] Hippocampus visualisation

Hi Freesurfer experts, I've run the subfield analysis with Dev v6 and am just wondering if it is possible to display only certain subfields (say the CA1 and Subiculum rendered in 3D using freeview? Can I also render the entire hippocampus that is basically the addition of all the subfields gi

Re: [Freesurfer] Parcellation stats

Hi Bruce, I have used the following command line: mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum and got the following: # ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 0 15766121 15766121.0 Seg 2 2182848